Author: bugman
Date: Wed Oct 15 13:41:12 2014
New Revision: 26288
URL: http://svn.gna.org/viewcvs/relax?rev=26288&view=rev
Log:
Added extensive sectioning printouts to the dauvergne_protocol model-free
auto-analysis.
The lib.text.section functions title() and subtitle() are now used to mark
out all parts of the
auto-analysis. This will allow for a much better understanding of the log
files produced by this
auto-analysis.
Modified:
trunk/auto_analyses/dauvergne_protocol.py
Modified: trunk/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/dauvergne_protocol.py?rev=26288&r1=26287&r2=26288&view=diff
==============================================================================
--- trunk/auto_analyses/dauvergne_protocol.py (original)
+++ trunk/auto_analyses/dauvergne_protocol.py Wed Oct 15 13:41:12 2014
@@ -31,6 +31,7 @@
from info import Info_box; info = Info_box()
from lib.errors import RelaxError, RelaxNoSequenceError, RelaxNoValueError
from lib.float import floatAsByteArray
+from lib.text.sectioning import title, subtitle
from lib.text.string import LIST, PARAGRAPH, SECTION, SUBSECTION, TITLE,
to_docstring
from pipe_control.interatomic import interatomic_loop
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
@@ -154,6 +155,9 @@
@type conv_loop: bool
"""
+ # Printout.
+ title(file=sys.stdout, text="The dauvergne_protocol model-free
auto-analysis")
+
# Execution lock.
status.exec_lock.acquire(pipe_bundle, mode='auto-analysis')
@@ -252,6 +256,9 @@
def check_vars(self):
"""Check that the user has set the variables correctly."""
+ # Printout.
+ subtitle(file=sys.stdout, text="Auto-analysis variable checking")
+
# The pipe bundle.
if not isinstance(self.pipe_bundle, str):
raise RelaxError("The pipe bundle name '%s' is invalid." %
self.pipe_bundle)
@@ -343,11 +350,8 @@
def convergence(self):
"""Test for the convergence of the global model."""
- # Print out.
- print("\n\n\n")
- print("#####################")
- print("# Convergence tests #")
- print("#####################\n")
+ # Printout.
+ title(file=sys.stdout, text="Convergence testing")
# Maximum number of iterations reached.
if self.max_iter and self.round > self.max_iter:
@@ -500,7 +504,8 @@
base_dir = self.results_dir+sep+model
# Printout.
- sys.stdout.write("\n\nDetermining the next round of optimisation for
'%s': " % base_dir)
+ subtitle(file=sys.stdout, text="Determining the next round of
optimisation")
+ print("%-30s %s" % ("Base model directory:", base_dir))
# Catch if a file exists with the name of the directory.
if not isdir(base_dir) and access(base_dir, F_OK):
@@ -508,7 +513,8 @@
# If no directory exists, set the round to 'init' or 0.
if not isdir(base_dir):
- sys.stdout.write(" 0.\n\n")
+ print("%-30s %i" % ("Round:", 0))
+ print("The base directory does not exist.")
return 0
# Is the directory readable, writable, and executable.
@@ -524,7 +530,8 @@
# Set the round to 'init' or 0 if there is no directory called
'init'.
if 'init' not in dir_list:
- sys.stdout.write(" 0.\n\n")
+ print("%-30s %i" % ("Round:", 0))
+ print("No 'init' directory present in the base directory.")
return 0
# Create a list of all files which begin with 'round_'.
@@ -544,7 +551,8 @@
# No directories beginning with 'round_' exist, set the round to 1.
if not len(numbers):
- sys.stdout.write(" 1.\n\n")
+ print("%-30s %i" % ("Round:", 1))
+ print("No directories beginning with 'round_' exist.")
return 1
# The highest number.
@@ -568,11 +576,12 @@
# No round, so assume the initial state.
if complete_round == 0:
- sys.stdout.write(" 0.\n\n")
+ print("%-30s %i" % ("Round:", 0))
+ print("No opt/results files can be found.")
return 0
# Determine the number for the next round (add 1 to the highest
completed round).
- sys.stdout.write(" %i.\n\n" % complete_round + 1)
+ print("%-30s %i" % ("Round:", complete_round + 1))
return complete_round + 1
@@ -583,6 +592,9 @@
################
if self.diff_model == 'local_tm':
+ # Printout.
+ title(file=sys.stdout, text="Model MI - Local tm")
+
# Base directory to place files into.
self.base_dir = self.results_dir+'local_tm'+sep
@@ -597,6 +609,16 @@
#############################
elif self.diff_model == 'sphere' or self.diff_model == 'prolate' or
self.diff_model == 'oblate' or self.diff_model == 'ellipsoid':
+ # Printout.
+ if self.diff_model == 'sphere':
+ title(file=sys.stdout, text="Model MII - Spherical
diffusion")
+ elif self.diff_model == 'prolate':
+ title(file=sys.stdout, text="Model MIII - Prolate spheroidal
diffusion")
+ elif self.diff_model == 'oblate':
+ title(file=sys.stdout, text="Model MIV - Oblate spheroidal
diffusion")
+ elif self.diff_model == 'ellipsoid':
+ title(file=sys.stdout, text="Model MV - Ellipsoidal
diffusion")
+
# No local_tm directory!
dir_list = listdir(self.results_dir)
if 'local_tm' not in dir_list:
@@ -614,6 +636,9 @@
# Inital round of optimisation for diffusion models MII to
MV.
if self.round == 0:
+ # Printout.
+ subtitle(file=sys.stdout, text="Initial round of
optimisation")
+
# Base directory to place files into.
self.base_dir =
self.results_dir+self.diff_model+sep+'init'+sep
@@ -656,6 +681,9 @@
# Normal round of optimisation for diffusion models MII to
MV.
else:
+ # Printout.
+ subtitle(file=sys.stdout, text="Round %i of
optimisation" % self.round)
+
# Base directory to place files into.
self.base_dir = self.results_dir+self.diff_model +
sep+'round_'+repr(self.round)+sep
@@ -693,8 +721,14 @@
############
elif self.diff_model == 'final':
+ # Printout.
+ title(file=sys.stdout, text="Final run")
+
# Diffusion model selection.
############################
+
+ # Printout.
+ subtitle(file=sys.stdout, text="Diffusion model selection")
# The contents of the results directory.
dir_list = listdir(self.results_dir)
@@ -757,6 +791,9 @@
# Monte Carlo simulations.
##########################
+ # Printout.
+ subtitle(file=sys.stdout, text="Monte Carlo simulations")
+
# Fix the diffusion tensor, if it exists.
if hasattr(get_pipe(self.name_pipe('final')), 'diff_tensor'):
self.interpreter.fix('diff')
@@ -772,6 +809,9 @@
# Write the final results.
##########################
+
+ # Printout.
+ subtitle(file=sys.stdout, text="Writing the final results")
# Create results files and plots of the data.
self.write_results()
r26288 - /trunk/auto_analyses/dauvergne_protocol.py