Author: bugman
Date: Mon Jun 4 19:38:26 2012
New Revision: 16647
URL: http://svn.gna.org/viewcvs/relax?rev=16647&view=rev
Log:
Updated the dauvergne_protocol auto-analysis to spawn all pipes into the
named bundle.
Modified:
branches/uf_redesign/auto_analyses/dauvergne_protocol.py
branches/uf_redesign/sample_scripts/model_free/dauvergne_protocol.py
branches/uf_redesign/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
Modified: branches/uf_redesign/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/auto_analyses/dauvergne_protocol.py?rev=16647&r1=16646&r2=16647&view=diff
==============================================================================
--- branches/uf_redesign/auto_analyses/dauvergne_protocol.py (original)
+++ branches/uf_redesign/auto_analyses/dauvergne_protocol.py Mon Jun 4
19:38:26 2012
@@ -120,10 +120,13 @@
opt_func_tol = 1e-25
opt_max_iterations = int(1e7)
- def __init__(self, pipe_name=None, results_dir=None, diff_model=None,
mf_models=['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'],
local_tm_models=['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7',
'tm8', 'tm9'], grid_inc=11, diff_tensor_grid_inc={'sphere': 11, 'prolate':
11, 'oblate': 11, 'ellipsoid': 6}, min_algor='newton', mc_sim_num=500,
max_iter=None, user_fns=None, conv_loop=True):
+ def __init__(self, pipe_name=None, pipe_bundle=None, results_dir=None,
diff_model=None, mf_models=['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7',
'm8', 'm9'], local_tm_models=['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5',
'tm6', 'tm7', 'tm8', 'tm9'], grid_inc=11, diff_tensor_grid_inc={'sphere': 11,
'prolate': 11, 'oblate': 11, 'ellipsoid': 6}, min_algor='newton',
mc_sim_num=500, max_iter=None, user_fns=None, conv_loop=True):
"""Perform the full model-free analysis protocol of d'Auvergne and
Gooley, 2008b.
@keyword pipe_name: The name of the data pipe containing
the sequence info. This data pipe should have all values set including the
CSA value, the bond length, the heteronucleus name and proton name. It
should also have all relaxation data loaded.
+ @type pipe_name: str
+ @keyword pipe_bundle: The data pipe bundle to associate
all spawned data pipes with.
+ @type pipe_bundle: str
@keyword results_dir: The directory, where files are saved
in.
@type results_dir: str
@keyword diff_model: The global diffusion model to
optimise. This can be one of 'local_tm', 'sphere', 'oblate', 'prolate',
'ellipsoid', or 'final'. If all or a subset of these are supplied as a list,
then these will be automatically looped over and calculated.
@@ -149,10 +152,11 @@
"""
# Execution lock.
- status.exec_lock.acquire(pipe_name, mode='auto-analysis')
+ status.exec_lock.acquire(pipe_bundle, mode='auto-analysis')
# Store the args.
self.pipe_name = pipe_name
+ self.pipe_bundle = pipe_bundle
self.mf_models = mf_models
self.local_tm_models = local_tm_models
self.grid_inc = grid_inc
@@ -202,7 +206,7 @@
sleep(1)
# Set the global model name.
- status.auto_analysis[self.pipe_name].diff_model =
self.diff_model
+ status.auto_analysis[self.pipe_bundle].diff_model =
self.diff_model
# Initialise the convergence data structures.
self.conv_data = Container()
@@ -225,13 +229,17 @@
# Clean up.
finally:
# Finish and unlock execution.
- status.auto_analysis[self.pipe_name].fin = True
+ status.auto_analysis[self.pipe_bundle].fin = True
status.current_analysis = None
status.exec_lock.release()
def check_vars(self):
"""Check that the user has set the variables correctly."""
+
+ # The pipe bundle.
+ if not isinstance(self.pipe_bundle, str):
+ raise RelaxError("The pipe bundle name '%s' is invalid." %
self.pipe_bundle)
# The diff model.
valid_models = ['local_tm', 'sphere', 'oblate', 'prolate',
'ellipsoid', 'final']
@@ -448,7 +456,7 @@
print("\nConvergence:")
if converged:
# Update the status.
- status.auto_analysis[self.pipe_name].convergence = True
+ status.auto_analysis[self.pipe_bundle].convergence = True
# Print out.
print(" [ Yes ]")
@@ -556,7 +564,7 @@
while True:
# Determine which round of optimisation to do (init,
round_1, round_2, etc).
self.round = self.determine_rnd(model=self.diff_model)
- status.auto_analysis[self.pipe_name].round = self.round
+ status.auto_analysis[self.pipe_bundle].round = self.round
# Inital round of optimisation for diffusion models MII to
MV.
if self.round == 0:
@@ -569,7 +577,7 @@
# Create the data pipe (deleting the old one if it
exists).
if has_pipe(name):
self.interpreter.pipe.delete(name)
- self.interpreter.pipe.create(name, 'mf')
+ self.interpreter.pipe.create(name, 'mf',
bundle=self.pipe_bundle)
# Load the local tm diffusion model MI results.
self.interpreter.results.read(file='results',
dir=self.results_dir+'local_tm'+sep+'aic')
@@ -632,7 +640,7 @@
break
# Unset the status.
- status.auto_analysis[self.pipe_name].round = None
+ status.auto_analysis[self.pipe_bundle].round = None
# Final run.
@@ -646,7 +654,7 @@
self.pipes = ['local_tm', 'sphere', 'prolate', 'oblate',
'ellipsoid']
# Remove all temporary pipes used in this auto-analysis.
- for name in pipe_names():
+ for name in pipe_names(bundle=self.pipe_bundle):
if name in self.pipes + self.mf_models +
self.local_tm_models + ['aic', 'previous']:
self.interpreter.pipe.delete(name)
@@ -657,7 +665,7 @@
raise RelaxError("The %s model must be optimised first."
% name)
# Create the local_tm data pipe.
- self.interpreter.pipe.create('local_tm', 'mf')
+ self.interpreter.pipe.create('local_tm', 'mf',
bundle=self.pipe_bundle)
# Load the local tm diffusion model MI results.
self.interpreter.results.read(file='results',
dir=self.results_dir+'local_tm'+sep+'aic')
@@ -678,7 +686,7 @@
raise RelaxError("Multiple rounds of optimisation of the
" + name + " (between 8 to 15) are required for the proper execution of this
script.")
# Create the data pipe.
- self.interpreter.pipe.create(model, 'mf')
+ self.interpreter.pipe.create(model, 'mf',
bundle=self.pipe_bundle)
# Load the diffusion model results.
self.interpreter.results.read(file='results',
dir=self.results_dir+model + sep+'round_'+repr(self.round)+sep+'opt')
@@ -723,7 +731,7 @@
# Create the data pipe for the previous data (deleting the old data
pipe first if necessary).
if has_pipe('previous'):
self.interpreter.pipe.delete('previous')
- self.interpreter.pipe.create('previous', 'mf')
+ self.interpreter.pipe.create('previous', 'mf',
bundle=self.pipe_bundle)
# Load the optimised diffusion tensor from the initial round.
if self.round == 1:
@@ -759,7 +767,7 @@
# Loop over the data pipes.
for name in self.pipes:
# Place the model name into the status container.
- status.auto_analysis[self.pipe_name].current_model = name
+ status.auto_analysis[self.pipe_bundle].current_model = name
# Create the data pipe (by copying).
if has_pipe(name):
@@ -787,36 +795,36 @@
self.interpreter.results.write(file='results', dir=dir,
force=True)
# Unset the status.
- status.auto_analysis[self.pipe_name].current_model = None
+ status.auto_analysis[self.pipe_bundle].current_model = None
def status_setup(self):
"""Initialise the status object."""
# Initialise the status object for this auto-analysis.
- status.init_auto_analysis(self.pipe_name, type='dauvergne_protocol')
- status.current_analysis = self.pipe_name
+ status.init_auto_analysis(self.pipe_bundle,
type='dauvergne_protocol')
+ status.current_analysis = self.pipe_bundle
# The global diffusion model.
- status.auto_analysis[self.pipe_name].diff_model = None
+ status.auto_analysis[self.pipe_bundle].diff_model = None
# The round of optimisation, i.e. the global iteration.
- status.auto_analysis[self.pipe_name].round = None
+ status.auto_analysis[self.pipe_bundle].round = None
# The list of model-free local tm models for optimisation, i.e. the
global iteration.
- status.auto_analysis[self.pipe_name].local_tm_models =
self.local_tm_models
+ status.auto_analysis[self.pipe_bundle].local_tm_models =
self.local_tm_models
# The list of model-free models for optimisation, i.e. the global
iteration.
- status.auto_analysis[self.pipe_name].mf_models = self.mf_models
+ status.auto_analysis[self.pipe_bundle].mf_models = self.mf_models
# The current model-free model.
- status.auto_analysis[self.pipe_name].current_model = None
+ status.auto_analysis[self.pipe_bundle].current_model = None
# The maximum number of iterations of the global model.
- status.auto_analysis[self.pipe_name].max_iter = self.max_iter
+ status.auto_analysis[self.pipe_bundle].max_iter = self.max_iter
# The convergence of the global model.
- status.auto_analysis[self.pipe_name].convergence = False
+ status.auto_analysis[self.pipe_bundle].convergence = False
def write_results(self):
Modified: branches/uf_redesign/sample_scripts/model_free/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/sample_scripts/model_free/dauvergne_protocol.py?rev=16647&r1=16646&r2=16647&view=diff
==============================================================================
--- branches/uf_redesign/sample_scripts/model_free/dauvergne_protocol.py
(original)
+++ branches/uf_redesign/sample_scripts/model_free/dauvergne_protocol.py Mon
Jun 4 19:38:26 2012
@@ -176,8 +176,9 @@
# The following sequence of user function calls can be changed as needed.
# Create the data pipe.
-name = "mf (%s)" % asctime(localtime())
-pipe.create(name, 'mf')
+pipe_bundle = "mf (%s)" % asctime(localtime())
+name = "origin"
+pipe.create(name, 'mf', bundle=pipe_bundle)
# Load the sequence.
sequence.read(file='noe.500.out', dir=None, mol_name_col=None,
res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None)
@@ -213,4 +214,4 @@
############
# Do not change!
-dAuvergne_protocol(pipe_name=name, diff_model=DIFF_MODEL,
mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC,
min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, conv_loop=CONV_LOOP)
+dAuvergne_protocol(pipe_name=name, pipe_bundle=pipe_bundle,
diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS,
grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM,
conv_loop=CONV_LOOP)
Modified:
branches/uf_redesign/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py?rev=16647&r1=16646&r2=16647&view=diff
==============================================================================
---
branches/uf_redesign/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
(original)
+++
branches/uf_redesign/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
Mon Jun 4 19:38:26 2012
@@ -179,8 +179,9 @@
# The following sequence of user function calls can be changed as needed.
# Create the data pipe.
-name = "mf (%s)" % asctime(localtime())
-pipe.create(name, 'mf')
+bundle_name = "mf (%s)" % asctime(localtime())
+name = "origin"
+pipe.create(name, 'mf', bundle=bundle_name)
# The data path.
data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' +
sep + 'model_free' + sep + 'sphere' + sep
@@ -226,4 +227,4 @@
# Loop over all global models.
for global_model in ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid',
'final']:
- dAuvergne_protocol(pipe_name=name, results_dir=results_dir,
diff_model=global_model, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC,
diff_tensor_grid_inc={'sphere': 5, 'prolate': 5, 'oblate': 5, 'ellipsoid':
3}, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, max_iter=1, conv_loop=CONV_LOOP)
+ dAuvergne_protocol(pipe_name=name, pipe_bundle=bundle_name,
results_dir=results_dir, diff_model=global_model, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC,
diff_tensor_grid_inc={'sphere': 5, 'prolate': 5, 'oblate': 5, 'ellipsoid':
3}, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, max_iter=1, conv_loop=CONV_LOOP)
r16647 - in /branches/uf_redesign: auto_analyses/ sample_scripts/model_free/ test_suite/system_tests/scripts/model_free/