Author: tlinnet
Date: Wed May 21 18:11:52 2014
New Revision: 23313
URL: http://svn.gna.org/viewcvs/relax?rev=23313&view=rev
Log:
Merged revisions 23310-23312 via svnmerge from
svn+ssh://tlinnet@xxxxxxxxxxx/svn/relax/trunk
........
r23310 | tlinnet | 2014-05-21 17:43:47 +0200 (Wed, 21 May 2014) | 6 lines
Modified system test Relax_disp.test_cpmg_synthetic_ns3d_to_cr72 to catch
bug.
bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all
numerical CPMG models.
Systemtest was renamed from test_cpmg_synthetic_cr72 to
test_cpmg_synthetic_ns3d_to_cr72, to
reflect which model create the data and which model fits the data.
........
r23311 | tlinnet | 2014-05-21 17:43:49 +0200 (Wed, 21 May 2014) | 6 lines
Modified cpmg_synthetic script to first create all time structures before
doing back-calculation.
bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all
numerical CPMG models.
The numerical models need all time points which are defined in setup, to be
present
when calculating.
........
r23312 | tlinnet | 2014-05-21 18:00:19 +0200 (Wed, 21 May 2014) | 5 lines
Renamed systemtest to test_cpmg_synthetic_ns3d_to_cr72_noise_cluster.
The model that creates the data has been changed to numerical model.
bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all
numerical CPMG models.
........
Modified:
branches/disp_speed/ (props changed)
branches/disp_speed/test_suite/system_tests/relax_disp.py
branches/disp_speed/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
Propchange: branches/disp_speed/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed May 21 18:11:52 2014
@@ -1 +1 @@
-/trunk:1-23304
+/trunk:1-23312
Modified: branches/disp_speed/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/system_tests/relax_disp.py?rev=23313&r1=23312&r2=23313&view=diff
==============================================================================
--- branches/disp_speed/test_suite/system_tests/relax_disp.py (original)
+++ branches/disp_speed/test_suite/system_tests/relax_disp.py Wed May 21
18:11:52 2014
@@ -955,17 +955,18 @@
relax_disp.Relax_disp(pipe_name='origin - relax_disp (Sun Feb 23
19:36:51 2014)', pipe_bundle='relax_disp (Sun Feb 23 19:36:51 2014)',
results_dir=self.tmpdir, models=['R2eff', 'No Rex'], grid_inc=11,
mc_sim_num=2, modsel='AIC', pre_run_dir=pre_run_dir, insignificance=1.0,
numeric_only=True, mc_sim_all_models=False, eliminate=True)
- def test_cpmg_synthetic_cr72(self):
+ def test_cpmg_synthetic_ns3d_to_cr72(self):
"""Test synthetic cpmg data.
- This script will produce synthetic CPMG R2eff values according to
the selected model, and the fit the selected model.
+ This script will produce synthetic CPMG R2eff values according to
the NS CPMG 2-site 3D model, and the fit the data with CR72.
"""
# Reset.
#self.interpreter.reset()
## Set Experiments.
- model_create = 'CR72'
+ model_create = 'NS CPMG 2-site 3D'
+ #model_create = 'NS CPMG 2-site expanded'
model_analyse = 'CR72'
# Exp 1
sfrq_1 = 599.8908617*1E6
@@ -986,7 +987,7 @@
exps = [exp_1, exp_2]
spins = [
- ['Ala', 1, 'N', {'r2': {r20_key_1:2, r20_key_2:2}, 'r2a':
{r20_key_1:2, r20_key_2:2}, 'r2b': {r20_key_1:2, r20_key_2:2}, 'kex': 1000,
'pA': 0.99, 'dw': 2} ]
+ ['Ala', 1, 'N', {'r2': {r20_key_1:10., r20_key_2:10.}, 'r2a':
{r20_key_1:10., r20_key_2:10.}, 'r2b': {r20_key_1:10., r20_key_2:10.}, 'kex':
1000., 'pA': 0.99, 'dw': 2.} ]
]
# Collect the data to be used.
@@ -1072,7 +1073,7 @@
print("###################################")
## Make test on R2.
- self.assertAlmostEqual(set_r2_frq, min_r2_frq, 6)
+ self.assertAlmostEqual(set_r2_frq, min_r2_frq, 2)
else:
grid_val = grid_params[mo_param]
min_val = min_params[mo_param]
@@ -1084,10 +1085,15 @@
print("###################################")
## Make test on parameters.
- self.assertAlmostEqual(set_val, min_val, 2)
-
-
- def test_cpmg_synthetic_cr72_full_noise_cluster(self):
+ if mo_param == 'dw':
+ self.assertAlmostEqual(set_val/10, min_val/10, 1)
+ elif mo_param == 'kex':
+ self.assertAlmostEqual(set_val/1000, min_val/1000, 1)
+ elif mo_param == 'pA':
+ self.assertAlmostEqual(set_val, min_val, 3)
+
+
+ def test_cpmg_synthetic_ns3d_to_cr72_noise_cluster(self):
"""Test synthetic cpmg data. For CR72 with small noise and cluster.
This script will produce synthetic CPMG R2eff values according to
the selected model, and the fit the selected model.
@@ -1097,7 +1103,8 @@
#self.interpreter.reset()
## Set Experiments.
- model_create = 'CR72'
+ model_create = 'NS CPMG 2-site 3D'
+ #model_create = 'NS CPMG 2-site expanded'
model_analyse = 'CR72'
# Exp 1
@@ -1121,8 +1128,8 @@
exps = [exp_1, exp_2]
spins = [
- ['Ala', 1, 'N', {'r2': {r20_key_1:10, r20_key_2:11.5}, 'r2a':
{r20_key_1:10, r20_key_2:11.5}, 'r2b': {r20_key_1:10, r20_key_2:11.5}, 'kex':
1000, 'pA': 0.99, 'dw': 2} ],
- ['Ala', 2, 'N', {'r2': {r20_key_1:13, r20_key_2:14.5}, 'r2a':
{r20_key_1:13, r20_key_2:14.5}, 'r2b': {r20_key_1:13, r20_key_2:14.5}, 'kex':
1000, 'pA': 0.99, 'dw': 1} ]
+ ['Ala', 1, 'N', {'r2': {r20_key_1:10., r20_key_2:11.5}, 'r2a':
{r20_key_1:10., r20_key_2:11.5}, 'r2b': {r20_key_1:10., r20_key_2:11.5},
'kex': 1000., 'pA': 0.99, 'dw': 2.} ],
+ ['Ala', 2, 'N', {'r2': {r20_key_1:13., r20_key_2:14.5}, 'r2a':
{r20_key_1:13., r20_key_2:14.5}, 'r2b': {r20_key_1:13., r20_key_2:14.5},
'kex': 1000., 'pA': 0.99, 'dw': 1.} ]
]
# Collect the data to be used.
@@ -1221,8 +1228,13 @@
print("WARNING: rel change level is above %.2f, and
is %.4f."%(ds.rel_change, rel_change))
print("###################################")
- ## Make test on parameters. Only if breaking the
relative change.
- self.assertAlmostEqual(set_val, min_val, 1)
+ ## Make test on parameters.
+ if mo_param == 'dw':
+ self.assertAlmostEqual(set_val/10, min_val/10, 1)
+ elif mo_param == 'kex':
+ self.assertAlmostEqual(set_val/1000, min_val/1000, 1)
+ elif mo_param == 'pA':
+ self.assertAlmostEqual(set_val, min_val, 2)
def test_cpmg_synthetic_dx_map_points(self):
Modified:
branches/disp_speed/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py?rev=23313&r1=23312&r2=23313&view=diff
==============================================================================
---
branches/disp_speed/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
(original)
+++
branches/disp_speed/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
Wed May 21 18:11:52 2014
@@ -380,8 +380,8 @@
after = getattr(cur_spin, mo_param)
print(cur_spin.model, res_name, cur_spin_id, mo_param, before)
-## Now doing the back calculation of R2eff values.
-# First loop over the frequencies.
+####### Now doing the back calculation of R2eff values.
+# First create fake data and read it in.
for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
exp_id = exp_ids[mi]
exp = exps[mi]
@@ -409,10 +409,24 @@
# This is a trick, or else relax complains.
relax_disp.r2eff_read_spin(id=exp_id, spin_id=cur_spin_id,
file=file_name, dir=ds.tmpdir, disp_point_col=1, data_col=2, error_col=3)
+
+# Now back-calculate.
+for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
+ exp_id = exp_ids[mi]
+ exp = exps[mi]
+ sfrq, time_T2, ncycs, r2eff_errs = exp
+
+ # Then loop over the spins.
+ for res_name, res_num, spin_name, params in cur_spins:
+ cur_spin_id = ":%i@%s"%(res_num, spin_name)
+ cur_spin = return_spin(cur_spin_id)
+
### Now back calculate values from parameters, and stuff R2eff it
back.
print("Generating data with MODEL:%s, for spin id:%s"%(model_create,
cur_spin_id))
r2effs = optimisation.back_calc_r2eff(spin=cur_spin,
spin_id=cur_spin_id)
+ # Define file name
+ file_name = "%s%s.txt" % (exp_id, cur_spin_id .replace('#',
'_').replace(':', '_').replace('@', '_'))
file = open_write_file(file_name=file_name, dir=ds.resdir,
force=True)
## Loop over the R2eff structure
# Loop over the points.
r23313 - in /branches/disp_speed: ./ test_suite/system_tests/ test_suite/system_tests/scripts/relax_disp/