Author: bugman
Date: Tue Feb 25 09:22:19 2014
New Revision: 22297
URL: http://svn.gna.org/viewcvs/relax?rev=22297&view=rev
Log:
Merged revisions 22291-22294 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r22291 | tlinnet | 2014-02-24 17:06:33 +0100 (Mon, 24 Feb 2014) | 5 lines
Modified unit test to pass.
Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG
analysis with two fields at two delay times.
Implemented as suggested in:
https://mail.gna.org/public/relax-devel/2014-02/msg00142.html
........
r22292 | tlinnet | 2014-02-24 17:06:35 +0100 (Mon, 24 Feb 2014) | 5 lines
Expanded the loop_time function to optional take the offset and dispersion
point as input for restricting looping.
Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG
analysis with two fields at two delay times.
This is implemented as suggested in:
https://mail.gna.org/public/relax-devel/2014-02/msg00143.html
........
r22293 | tlinnet | 2014-02-24 17:06:36 +0100 (Mon, 24 Feb 2014) | 5 lines
Added system test for loop_time.
Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG
analysis with two fields at two delay times.
This system can be extended later for purposes to test the restriction of
the looping.
........
r22294 | tlinnet | 2014-02-24 18:28:11 +0100 (Mon, 24 Feb 2014) | 5 lines
Replacing looping over time points from cdp.relax_time_list to
loop_time(frq=frq).
Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG
analysis with two fields at two delay times.
loop_time has been modified to accept spectrometer frequency as input to
restrict the looping.
........
Modified:
branches/double_rotor/ (props changed)
branches/double_rotor/specific_analyses/relax_disp/api.py
branches/double_rotor/specific_analyses/relax_disp/disp_data.py
branches/double_rotor/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Propchange: branches/double_rotor/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Feb 25 09:22:19 2014
@@ -1,1 +1,1 @@
-/trunk:1-22289
+/trunk:1-22294
Modified: branches/double_rotor/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/relax_disp/api.py?rev=22297&r1=22296&r2=22297&view=diff
==============================================================================
--- branches/double_rotor/specific_analyses/relax_disp/api.py (original)
+++ branches/double_rotor/specific_analyses/relax_disp/api.py Tue Feb 25
09:22:19 2014
@@ -149,7 +149,7 @@
values = []
errors = []
times = []
- for time in cdp.relax_time_list:
+ for time in loop_time(frq=frq):
# The data.
values.append(average_intensity(spin=spin, exp_type=exp_type,
frq=frq, offset=offset, point=point, time=time))
errors.append(average_intensity(spin=spin, exp_type=exp_type,
frq=frq, offset=offset, point=point, time=time, error=True))
@@ -378,7 +378,7 @@
values = []
errors = []
times = []
- for time in cdp.relax_time_list:
+ for time in loop_time(frq=frq):
values.append(average_intensity(spin=spin,
exp_type=exp_type, frq=frq, offset=offset, point=point, time=time,
sim_index=sim_index))
errors.append(average_intensity(spin=spin,
exp_type=exp_type, frq=frq, offset=offset, point=point, time=time,
error=True))
times.append(time)
@@ -1373,7 +1373,7 @@
# Generate the data structure to return.
errors = []
- for time in cdp.relax_time_list:
+ for time in loop_time(frq=frq):
errors.append(average_intensity(spin=spin,
exp_type=exp_type, frq=frq, offset=offset, point=point, time=time,
error=True))
# All other models.
@@ -1597,7 +1597,7 @@
# Loop over each time point.
ti = 0
- for time in loop_time():
+ for time in loop_time(frq=frq):
# Get the intensity keys.
int_keys = find_intensity_keys(exp_type=exp_type, frq=frq,
point=point, time=time)
Modified: branches/double_rotor/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/relax_disp/disp_data.py?rev=22297&r1=22296&r2=22297&view=diff
==============================================================================
--- branches/double_rotor/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/double_rotor/specific_analyses/relax_disp/disp_data.py Tue Feb
25 09:22:19 2014
@@ -1281,13 +1281,17 @@
yield id
-def loop_time(exp_type=None, frq=None, return_indices=False):
+def loop_time(exp_type=None, frq=None, offset=None, point=None,
return_indices=False):
"""Generator method for looping over the relaxation times.
@keyword exp_type: The experiment type.
@type exp_type: str
@keyword frq: The spectrometer frequency in Hz.
@type frq: float
+ @keyword offset: The spin-lock or hard pulse offset value in
ppm.
+ @type offset: None or float
+ @keyword point: The dispersion point data (either the
spin-lock field strength in Hz or the nu_CPMG frequency in Hz).
+ @type point: float
@keyword return_indices: A flag which if True will cause the
relaxation time index to be returned as well.
@type return_indices: bool
@return: The relaxation time.
@@ -1310,6 +1314,25 @@
# Skip non-matching spectrometer frequencies.
if frq != None and hasattr(cdp, 'spectrometer_frq') and
cdp.spectrometer_frq[id] != frq:
continue
+
+ # Skip non-matching offsets.
+ if offset != None and hasattr(cdp, 'spin_lock_offset') and
cdp.spin_lock_offset[id] != offset:
+ continue
+
+ # The dispersion point filter.
+ if point != None:
+ # No experiment type set.
+ if not hasattr(cdp, 'exp_type') or id not in
cdp.exp_type:
+ continue
+
+ # The experiment type.
+ exp_type = cdp.exp_type[id]
+
+ # The CPMG dispersion data.
+ if exp_type in EXP_TYPE_LIST_CPMG:
+ # No dispersion point data set.
+ if not hasattr(cdp, 'cpmg_frqs') or id not in
cdp.cpmg_frqs:
+ continue
if time != cdp.relax_times[id]:
continue
@@ -1907,7 +1930,7 @@
set_labels.append("Spin %s" % id)
# Loop over the relaxation time periods.
- for time in cdp.relax_time_list:
+ for time in loop_time(frq=frq):
# The key.
keys = find_intensity_keys(exp_type=exp_type, frq=frq,
point=point, time=time)
Modified:
branches/double_rotor/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py?rev=22297&r1=22296&r2=22297&view=diff
==============================================================================
---
branches/double_rotor/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
(original)
+++
branches/double_rotor/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Tue Feb 25 09:22:19 2014
@@ -25,7 +25,7 @@
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from pipe_control import state
-from specific_analyses.relax_disp.disp_data import loop_exp_frq,
loop_exp_frq_offset, loop_exp_frq_offset_point, loop_exp_frq_offset_point_time
+from specific_analyses.relax_disp.disp_data import loop_exp_frq,
loop_exp_frq_offset, loop_exp_frq_offset_point,
loop_exp_frq_offset_point_time, loop_time
from status import Status; status = Status()
from test_suite.unit_tests.base_classes import UnitTestCase
@@ -214,7 +214,7 @@
# Original indices (ei, mi, oi).
indices = [
[0, 0, 0, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16], 0],
- [0, 1, 0, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16], 1]
+ [0, 1, 0, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16], 0]
]
# Check the number of iterations.
@@ -291,3 +291,38 @@
j += 1
self.assertEqual(time, time_T2_2)
self.assertAlmostEqual(point, cpmg_2[j],3)
+
+
+ def test_loop_time(self):
+ """Unit test of the loop_time() function.
+
+ This uses the data of the saved state attached to U{bug
#21665<https://gna.org/bugs/?21665>}.
+ """
+
+ # Load the state.
+ statefile = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21665.bz2'
+ state.load_state(statefile, force=True)
+
+ # Original data (exp_type, frq, offset, point).
+ data = [
+ ['SQ CPMG', 499862140.0, 0, [50.0, 100.0, 150.0, 200.0, 250.0,
300.0, 350.0, 400.0, 450.0, 500.0, 550.0, 600.0, 650.0, 700.0, 800.0, 900.0,
1000.0],0.04],
+ ['SQ CPMG', 599890858.69999993, 0, [33.3333, 66.666, 100.0,
133.333, 166.666, 200.0, 233.333, 266.666, 300.0, 333.333, 366.666, 400.0,
466.666, 533.333, 666.666, 866.666, 1000.0],0.06]
+ ]
+
+ # Original indices (ei, mi, oi, ti).
+ indices = [
+ [0, 0, 0, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16], 0],
+ [0, 1, 0, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16], 0]
+ ]
+
+ # Check the number of iterations.
+ print("Checking the number of iterations of the loop.")
+ count_frq = 0
+ for dat in data:
+ frq = dat[1]
+ for time, ti in loop_time(frq=frq, return_indices=True):
+ print(time, ti)
+ count_frq += 1
+ self.assertEqual(count_frq, 2)
+
+
r22297 - in /branches/double_rotor: ./ specific_analyses/relax_disp/ test_suite/unit_tests/_specific_analyses/_relax_disp/