Author: tlinnet
Date: Wed Jul 30 22:27:28 2014
New Revision: 24863
URL: http://svn.gna.org/viewcvs/relax?rev=24863&view=rev
Log:
Code validation of systemtest file for Relax_disp.
sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
Modified:
branches/r1rho_plotting/test_suite/system_tests/relax_disp.py
Modified: branches/r1rho_plotting/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/r1rho_plotting/test_suite/system_tests/relax_disp.py?rev=24863&r1=24862&r2=24863&view=diff
==============================================================================
--- branches/r1rho_plotting/test_suite/system_tests/relax_disp.py
(original)
+++ branches/r1rho_plotting/test_suite/system_tests/relax_disp.py Wed
Jul 30 22:27:28 2014
@@ -239,9 +239,7 @@
def setup_r1rho_kjaergaard(self, cluster_ids=[], read_R1=True):
- """Set up the data for the test_r1rho_kjaergaard_*() system tests.
-
- """
+ """Set up the data for the test_r1rho_kjaergaard_*() system tests."""
# The path to the data files.
data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
@@ -249,7 +247,7 @@
# Set pipe name, bundle and type.
ds.pipe_name = 'base pipe'
ds.pipe_bundle = 'relax_disp'
- ds.pipe_type= 'relax_disp'
+ ds.pipe_type = 'relax_disp'
# Create the data pipe.
self.interpreter.pipe.create(pipe_name=ds.pipe_name,
bundle=ds.pipe_bundle, pipe_type=ds.pipe_type)
@@ -284,7 +282,7 @@
# Count settings
j = 0
for i in range(len(expfileslines)):
- line=expfileslines[i]
+ line = expfileslines[i]
if line[0] == "#":
continue
else:
@@ -787,10 +785,10 @@
# Set up the metadata for the experiments.
# This value is used in Baldwin.py. It is the 1H Larmor frequency.
- sfrq= 200. * 1E6
+ sfrq = 200. * 1E6
# Total time of CPMG block.
- Trelax=0.04
+ Trelax = 0.04
# First set the
for i in range(len(ids)):
@@ -900,7 +898,7 @@
grid_results.append([spin.r2[r20_key], spin.dw, spin.pA,
spin.kex, spin.chi2, spin_id, resi, resn])
## Now do minimisation.
- # Standard parameters are: func_tol=1e-25, grad_tol=None,
max_iter=10000000,
+ # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
set_func_tol = 1e-10
set_max_iter = 1000
self.interpreter.minimise(min_algor='simplex',
func_tol=set_func_tol, max_iter=set_max_iter, constraints=True, scaling=True,
verbosity=1)
@@ -918,15 +916,15 @@
# Reference values from Baldwin.py.
# Exchange rate = k+ + k- (s-1)
- kex=1000.
+ kex = 1000.
# Fractional population of excited state k+/kex
- pb=0.01
+ pb = 0.01
# deltaOmega in ppm
- dw_ppm=2.
+ dw_ppm = 2.
#relaxation rate of ground (s-1)
- R2g=2.
+ R2g = 2.
#relaxation rate of excited (s-1)
- R2e=2.
+ R2e = 2.
# Test the parameters which created the data.
# This is for the 1H spin.
@@ -940,7 +938,8 @@
def test_baldwin_synthetic_full(self):
"""Test synthetic data of Andrew J. Baldwin B14 model. Support
requst sr #3154 U{https://gna.org/support/index.php?3154}.
- This uses the synthetic data from paper U{DOI:
10.1016/j.jmr.2014.02.023 <http://dx.doi.org/10.1016/j.jmr.2014.02.023>}."""
+ This uses the synthetic data from paper U{DOI:
10.1016/j.jmr.2014.02.023 <http://dx.doi.org/10.1016/j.jmr.2014.02.023>}.
+ """
# The path to the data files.
data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Baldwin_2014'
@@ -971,10 +970,10 @@
# Set up the metadata for the experiments.
# This value is used in Baldwin.py. It is the 1H Larmor frequency.
- sfrq= 200. * 1E6
+ sfrq = 200. * 1E6
# Total time of CPMG block.
- Trelax=0.04
+ Trelax = 0.04
# First set the
for i in range(len(ids)):
@@ -1085,7 +1084,7 @@
grid_results.append([spin.r2a[r20_key], spin.r2b[r20_key],
spin.dw, spin.pA, spin.kex, spin.chi2, spin_id, resi, resn])
## Now do minimisation.
- # Standard parameters are: func_tol=1e-25, grad_tol=None,
max_iter=10000000,
+ # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
set_func_tol = 1e-11
set_max_iter = 10000
self.interpreter.minimise(min_algor='simplex',
func_tol=set_func_tol, max_iter=set_max_iter, constraints=True, scaling=True,
verbosity=1)
@@ -1105,15 +1104,15 @@
# Reference values from Baldwin.py.
# Exchange rate = k+ + k- (s-1)
- kex=1000.
+ kex = 1000.
# Fractional population of excited state k+/kex
- pb=0.01
+ pb = 0.01
# deltaOmega in ppm
- dw_ppm=2.
+ dw_ppm = 2.
#relaxation rate of ground (s-1)
- R2g=2.
+ R2g = 2.
#relaxation rate of excited (s-1)
- R2e=100.
+ R2e = 100.
# Test the parameters which created the data.
# This is for the 1H spin.
@@ -4715,7 +4714,7 @@
MODSEL = 'AIC'
# Execute the auto-analysis (fast).
- # Standard parameters are: func_tol=1e-25, grad_tol=None,
max_iter=10000000,
+ # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
OPT_FUNC_TOL = 1e-1
relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL
OPT_MAX_ITERATIONS = 1000
@@ -4775,7 +4774,7 @@
MODSEL = 'AIC'
# Execute the auto-analysis (fast).
- # Standard parameters are: func_tol=1e-25, grad_tol=None,
max_iter=10000000,
+ # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
OPT_FUNC_TOL = 1e-1
relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL
OPT_MAX_ITERATIONS = 1000
@@ -4921,7 +4920,7 @@
MC_NUM = 3
# Execute the auto-analysis (fast).
- # Standard parameters are: func_tol=1e-25, grad_tol=None,
max_iter=10000000,
+ # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
OPT_FUNC_TOL = 1e-1
OPT_MAX_ITERATIONS = 1000
@@ -5119,7 +5118,7 @@
MODSEL = 'AIC'
# Execute the auto-analysis (fast).
- # Standard parameters are: func_tol=1e-25, grad_tol=None,
max_iter=10000000,
+ # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
OPT_FUNC_TOL = 1e-1
relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL
OPT_MAX_ITERATIONS = 1000
@@ -5536,7 +5535,7 @@
MODSEL = 'AIC'
# Execute the auto-analysis (fast).
- # Standard parameters are: func_tol=1e-25, grad_tol=None,
max_iter=10000000.
+ # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
OPT_FUNC_TOL = 1e-1
relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL
OPT_MAX_ITERATIONS = 1000
@@ -5663,7 +5662,7 @@
# Then select model.
self.interpreter.relax_disp.select_model(model=MODEL)
- # GRID inc of 7 was found to be appropriate not to find pA=0.5.
+ # GRID inc of 7 was found to be appropriate not to find pA = 0.5.
GRID_INC = 7
# Store grid and minimisations results.
@@ -5686,7 +5685,7 @@
grid_results.append([spin.r2[r20_key_600], spin.r2[r20_key_500],
spin.dw, spin.pA, spin.kex, spin.chi2, spin_id, resi, resn])
## Now do minimisation.
- # Standard parameters are: func_tol=1e-25, grad_tol=None,
max_iter=10000000,
+ # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
set_func_tol = 1e-9
set_max_iter = 100000
self.interpreter.minimise(min_algor='simplex',
func_tol=set_func_tol, max_iter=set_max_iter, constraints=True, scaling=True,
verbosity=1)
@@ -6577,7 +6576,7 @@
# Set pipe name, bundle and type.
pipe_name = 'base pipe'
pipe_bundle = 'relax_disp'
- pipe_type= 'relax_disp'
+ pipe_type = 'relax_disp'
# The path to the data files.
data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
@@ -6624,7 +6623,7 @@
MODSEL = 'AIC'
# Execute the auto-analysis (fast).
- # Standard parameters are: func_tol=1e-25, grad_tol=None,
max_iter=10000000,
+ # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
OPT_FUNC_TOL = 1e-1
relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL
OPT_MAX_ITERATIONS = 1000
r24863 - /branches/r1rho_plotting/test_suite/system_tests/relax_disp.py