Author: tlinnet
Date: Mon Jun 23 13:04:22 2014
New Revision: 24240
URL: http://svn.gna.org/viewcvs/relax?rev=24240&view=rev
Log:
Added unit test unit_tests/_lib/_dispersion/test_matrix_exponential.py to
test the matrix exponential from higher dimensional data.
- lib.dispersion.matrix_exponential.matrix_exponential_rankN
will match against
- lib.linear_algebra.matrix_exponential.
Data which is used for comparison, comes from system test:
Relax_disp.test_hansen_cpmg_data_to_ns_cpmg_2site_3D.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Added:
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py
Added:
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py?rev=24240&view=auto
==============================================================================
---
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py
(added)
+++
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py
Mon Jun 23 13:04:22 2014
@@ -0,0 +1,108 @@
+###############################################################################
+#
#
+# Copyright (C) 2014 Troels E. Linnet
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+# Python module imports.
+from os import path, sep
+from numpy import dot, einsum, load, sum
+from unittest import TestCase
+
+# relax module imports.
+from lib.dispersion.ns_matrices import rcpmg_3d_rankN
+from lib.linear_algebra.matrix_exponential import matrix_exponential
+from lib.dispersion.matrix_exponential import matrix_exponential_rankN
+from status import Status; status = Status()
+
+
+class Test_matrix_exponential(TestCase):
+ """Unit tests for the lib.dispersion.matrix_exponential relax module."""
+
+ def setUp(self):
+ """Set up for all unit tests."""
+
+ # Default parameter values.
+ self.data =
status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'unit_tests'+sep+'lib'+sep+'dispersion'+sep+'matrix_exponential'
+
+ def return_data(self, fname):
+ """Return the data structures from the data path."""
+
+ r180x = load(fname+"_r180x"+".npy")
+ M0 = load(fname+"_M0"+".npy")
+ r10a = load(fname+"_r10a"+".npy")
+ r10b = load(fname+"_r10b"+".npy")
+ r20a = load(fname+"_r20a"+".npy")
+ r20b = load(fname+"_r20b"+".npy")
+ pA = load(fname+"_pA"+".npy")
+ dw = load(fname+"_dw"+".npy")
+ dw_orig = load(fname+"_dw_orig"+".npy")
+ kex = load(fname+"_kex"+".npy")
+ inv_tcpmg = load(fname+"_inv_tcpmg"+".npy")
+ tcp = load(fname+"_tcp"+".npy")
+ num_points = load(fname+"_num_points"+".npy")
+ power = load(fname+"_power"+".npy")
+ back_calc = load(fname+"_back_calc"+".npy")
+
+ # Once off parameter conversions.
+ pB = 1.0 - pA
+ k_BA = pA * kex
+ k_AB = pB * kex
+
+ return r180x, M0, r10a, r10b, r20a, r20b, pA, dw, dw_orig, kex,
inv_tcpmg, tcp, num_points, power, back_calc, pB, k_BA, k_AB
+
+
+ def test_ns_cpmg_2site_3d_hansen_cpmg_data(self):
+ """Test the matrix_exponential_rankN() function for higher
dimensional data, and compare to matrix_exponential. This uses the data from
systemtest Relax_disp.test_hansen_cpmg_data_to_ns_cpmg_2site_3D."""
+
+ fname = self.data + sep+ "test_hansen_cpmg_data_to_ns_cpmg_2site_3D"
+ r180x, M0, r10a, r10b, r20a, r20b, pA, dw, dw_orig, kex, inv_tcpmg,
tcp, num_points, power, back_calc, pB, k_BA, k_AB = self.return_data(fname)
+
+ # Extract the total numbers of experiments, number of spins, number
of magnetic field strength, number of offsets, maximum number of dispersion
point.
+ NE, NS, NM, NO, ND = back_calc.shape
+
+ # The matrix R that contains all the contributions to the evolution,
i.e. relaxation, exchange and chemical shift evolution.
+ R_mat = rcpmg_3d_rankN(R1A=r10a, R1B=r10b, R2A=r20a, R2B=r20b,
pA=pA, pB=pB, dw=dw, k_AB=k_AB, k_BA=k_BA, tcp=tcp)
+
+ # This matrix is a propagator that will evolve the magnetization
with the matrix R for a delay tcp.
+ Rexpo_mat = matrix_exponential_rankN(R_mat)
+
+ # Loop over the spins
+ for si in range(NS):
+ # Loop over the spectrometer frequencies.
+ for mi in range(NM):
+ # Extract number of points.
+ num_points_si_mi = int(num_points[0, si, mi, 0])
+
+ # Loop over the time points, back calculating the R2eff
values.
+ for di in range(num_points_si_mi):
+ # Test the two different methods.
+ R_mat_i = R_mat[0, si, mi, 0, di]
+
+ # The lower dimensional matrix exponential.
+ Rexpo = matrix_exponential(R_mat_i)
+
+ # The higher dimensional matrix exponential.
+ Rexpo_mat_i = Rexpo_mat[0, si, mi, 0, di]
+
+ diff = Rexpo - Rexpo_mat_i
+ diff_sum = sum(diff)
+
+ # Test that the sum difference is zero.
+ self.assertAlmostEqual(diff_sum, 0.0)
+
r24240 - /branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py