Author: bugman
Date: Mon Oct 20 16:45:49 2014
New Revision: 26320
URL: http://svn.gna.org/viewcvs/relax?rev=26320&view=rev
Log:
The compression level for results files can now be set in the frame order
auto-analysis.
This is via the new argument results_compress_type, which is used to set the
compress_type argument
of the results.write user function. The results reading parts of the
auto-analysis have been
updated to allow uncompressed, bzip2 compressed, and gzip compressed files to
be handled.
Modified:
branches/frame_order_cleanup/auto_analyses/frame_order.py
Modified: branches/frame_order_cleanup/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/frame_order.py?rev=26320&r1=26319&r2=26320&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/frame_order.py (original)
+++ branches/frame_order_cleanup/auto_analyses/frame_order.py Mon Oct 20
16:45:49 2014
@@ -126,7 +126,13 @@
continue
# No file.
- if not access(dirs[i]+sep+'results.bz2', F_OK):
+ found = False
+ for ext in ['.bz2', '', 'gz']:
+ file = dirs[i]+sep+'results'+ext
+ if access(file, F_OK):
+ found = True
+ break
+ if not found:
continue
# Create a data pipe.
@@ -265,7 +271,13 @@
contents2 = []
for i in range(len(models)):
# No file.
- if not access(dirs[i]+sep+'results.bz2', F_OK):
+ found = False
+ for ext in ['.bz2', '', 'gz']:
+ file = dirs[i]+sep+'results'+ext
+ if access(file, F_OK):
+ found = True
+ break
+ if not found:
continue
# Create a data pipe.
@@ -369,7 +381,7 @@
# Debugging and test suite variables.
_final_state = True
- def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, pre_run_dir=None, opt_rigid=None,
opt_subset=None, opt_full=None, opt_mc=None, mc_sim_num=500,
models=MODEL_LIST_NONREDUNDANT, brownian_step_size=2.0, brownian_snapshot=10,
brownian_total=1000, rigid_grid_split=False, store_intermediate=True):
+ def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, pre_run_dir=None, opt_rigid=None,
opt_subset=None, opt_full=None, opt_mc=None, mc_sim_num=500,
models=MODEL_LIST_NONREDUNDANT, brownian_step_size=2.0, brownian_snapshot=10,
brownian_total=1000, results_compress_type=0, rigid_grid_split=False,
store_intermediate=True):
"""Perform the full frame order analysis.
@param data_pipe_full: The name of the data pipe containing
all of the RDC and PCS data.
@@ -400,6 +412,8 @@
@type brownian_snapshot: int
@keyword brownian_total: The total argument for the
pseudo-Brownian dynamics simulation frame_order.simulate user function.
@type brownian_total: int
+ @keyword results_compress_type: The type of compression to use when
creating the results files. See the results.write user function for details.
+ @type results_compress_type: int
@keyword rigid_grid_split: A flag which if True will cause the
grid search for the rigid model to be split so that the rotation is optimised
first followed by the translation. When combined with grid zooming, this can
save optimisation time. However it may result in the global minimum being
missed.
@type rigid_grid_split: bool
@keyword store_intermediate: A flag which if True will cause all
intermediate optimisation results to be stored in the 'intermediate_results'
directory. These can then be used for studying the optimisation settings or
loaded for subsequent analyses.
@@ -426,6 +440,7 @@
self.brownian_step_size = brownian_step_size
self.brownian_snapshot = brownian_snapshot
self.brownian_total = brownian_total
+ self.results_compress_type = results_compress_type
self.rigid_grid_split = rigid_grid_split
self.store_intermediate = store_intermediate
@@ -1275,23 +1290,33 @@
base_dir = self.results_dir
if pre_run:
base_dir = self.pre_run_dir
- path = model_directory(model, base_dir=base_dir) + sep +
'results.bz2'
-
- # The file does not exist.
- if not access(path, F_OK):
- return False
-
- # Create an empty data pipe.
- self.interpreter.pipe.create(pipe_name=pipe_name, pipe_type='frame
order')
-
- # Read the results file.
- self.interpreter.results.read(path)
-
- # Results printout.
- self.print_results()
+ path = model_directory(model, base_dir=base_dir) + sep + 'results'
+
+ # Loop over the compression types.
+ found = False
+ for ext in ['.bz2', '', 'gz']:
+ # The full file name.
+ full_path = path + ext
+
+ # The file does not exist.
+ if not access(full_path, F_OK):
+ continue
+
+ # Create an empty data pipe.
+ self.interpreter.pipe.create(pipe_name=pipe_name,
pipe_type='frame order')
+
+ # Read the results file.
+ self.interpreter.results.read(full_path)
+
+ # Results printout.
+ self.print_results()
+
+ # The flag.
+ found = True
+ break
# Success.
- return True
+ return found
def reorder_models(self, models=None):
@@ -1366,7 +1391,7 @@
# The results file.
if results_file:
- self.interpreter.results.write(dir=dir, force=True)
+ self.interpreter.results.write(dir=dir,
compress_type=self.results_compress_type, force=True)
# The RDC and PCS correlation plots.
self.interpreter.rdc.corr_plot(dir=dir, force=True)
r26320 - /branches/frame_order_cleanup/auto_analyses/frame_order.py