Author: tlinnet
Date: Thu Mar 6 17:11:18 2014
New Revision: 22414
URL: http://svn.gna.org/viewcvs/relax?rev=22414&view=rev
Log:
Added unit test for return_offset_data.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This is development according to thread
http://thread.gmane.org/gmane.science.nmr.relax.devel/5157.
Modified:
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Modified:
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py?rev=22414&r1=22413&r2=22414&view=diff
==============================================================================
---
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
(original)
+++
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Thu Mar 6 17:11:18 2014
@@ -25,9 +25,11 @@
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
+from math import atan, pi
from pipe_control import state
+from pipe_control.mol_res_spin import get_spin_ids, return_spin
from specific_analyses.relax_disp.checks import get_times
-from specific_analyses.relax_disp.disp_data import count_relax_times,
find_intensity_keys, get_curve_type, has_exponential_exp_type, loop_exp_frq,
loop_exp_frq_offset, loop_exp_frq_offset_point,
loop_exp_frq_offset_point_time, loop_time
+from specific_analyses.relax_disp.disp_data import count_relax_times,
find_intensity_keys, get_curve_type, has_exponential_exp_type, loop_exp_frq,
loop_exp_frq_offset, loop_exp_frq_offset_point,
loop_exp_frq_offset_point_time, loop_time, return_offset_data,
return_spin_lock_nu1
from status import Status; status = Status()
from test_suite.unit_tests.base_classes import UnitTestCase
@@ -676,3 +678,72 @@
count += 1
+ def test_return_offset_data(self):
+ """Unit test of the return_offset_data() function for R1rho setup.
+
+ This uses the data of the saved state attached to U{bug
#21344<https://gna.org/bugs/?21344>}.
+ """
+
+ # Load the state.
+ statefile = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21344_trunc.bz2'
+ state.load_state(statefile, force=True)
+
+ # Get the field count
+ field_count = cdp.spectrometer_frq_count
+
+ # Get the spin_lock_field points
+ spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
+
+ # Initialize data containers
+ all_spin_ids = get_spin_ids()
+
+ # Containers for only selected spins
+ cur_spin_ids = []
+ cur_spins = []
+ for curspin_id in all_spin_ids:
+ # Get the spin
+ curspin = return_spin(curspin_id)
+
+ # Check if is selected
+ if curspin.select == True:
+ cur_spin_ids.append(curspin_id)
+ cur_spins.append(curspin)
+
+ # Get the spectometer frequency
+ sfrq = cdp.spectrometer_frq_list[0]
+
+ # In MHz
+ yOBS = 81.050
+ # In ppm
+ yCAR = 118.078
+ centerPPM_N15 = yCAR
+
+ # Gyromagnetic ratios
+ g1H = 26.7522212 * 1e7
+ g15N = -2.7126 * 1e7
+
+ # The offset and R1 data.
+ chemical_shifts, offsets, tilt_angles =
return_offset_data(spins=cur_spins, spin_ids=cur_spin_ids,
field_count=field_count, fields=spin_lock_nu1)
+
+ # Loop over the index of spins, then exp_type, frq, offset
+ print("Printing the following")
+ print("exp_type curspin_id frq offset{ppm}
offsets[ei][si][mi][oi]{rad/s} ei mi oi si di cur_spin.chemical_shift{ppm}
chemical_shifts[ei][si][mi]{rad/s} spin_lock_nu1{Hz}
tilt_angles[ei][si][mi][oi]{rad}")
+ for si in range(len(cur_spin_ids)):
+ curspin_id = cur_spin_ids[si]
+ cur_spin = cur_spins[si]
+ for exp_type, frq, offset, ei, mi, oi in
loop_exp_frq_offset(return_indices=True):
+ # Loop over the dispersion points.
+ spin_lock_fields = spin_lock_nu1[ei][mi][oi]
+ for di in range(len(spin_lock_fields)):
+ print("%-8s %-10s %11.1f %8.4f %12.5f %i %i %i %i %i
%7.3f %12.5f %12.5f %12.5f"%(exp_type, curspin_id, frq, offset,
offsets[ei][si][mi][oi], ei, mi, oi, si, di, cur_spin.chemical_shift,
chemical_shifts[ei][si][mi], spin_lock_fields[di],
tilt_angles[ei][si][mi][oi][di]))
+ # Test chemical shift conversion
+ self.assertEqual(chemical_shifts[ei][si][mi],
cur_spin.chemical_shift * 2.0 * pi * sfrq / g1H * g15N * 1e-6)
+ # Test the offset conversion
+ self.assertEqual(offsets[ei][si][mi][oi], offset * 2.0 *
pi * sfrq / g1H * g15N * 1e-6)
+ # Test the tiltangle
+ c_omega1 = spin_lock_fields[di] * 2.0 * pi
+ c_Delta_omega = chemical_shifts[ei][si][mi] -
offsets[ei][si][mi][oi]
+ c_theta = atan(c_omega1 / c_Delta_omega)
+ self.assertEqual(tilt_angles[ei][si][mi][oi][di],
c_theta)
+
+
r22414 - /trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py