Source code for brainvisa.axon.processes
# -*- coding: utf-8 -*-
#
# This software and supporting documentation were developed by
# CEA/DSV/SHFJ and IFR 49
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#
# This software is governed by the CeCILL license version 2 under
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# You can use, modify and/or redistribute the software under the
# terms of the CeCILL license version 2 as circulated by CEA, CNRS
# and INRIA at the following URL "http://www.cecill.info".
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# same conditions as regards security.
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# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license version 2 and that you accept its terms.
# This script is intended to get run using BrainVISA (BV) script support ('-e'
# option). A independent GUI is displayed from BV and operates processes.
from __future__ import print_function
from __future__ import absolute_import
import brainvisa.axon
import atexit
import os
import sys
from brainvisa.configuration import neuroConfig
import brainvisa.processes
from brainvisa.data import neuroHierarchy, neuroData, temporary
from brainvisa.data.minfExtensions import initializeMinfExtensions
import brainvisa.toolboxes
from brainvisa.processing import neuroException, neuroLog
# the environment has to contain everything necessary as neuroConfig
# used to do: import many things here...
from brainvisa.processes import *
import six
_count = 0
[docs]def cleanup():
"""
Cleanup to be done at Brainvisa exiting. This function is registered in atexit.
"""
# cleanup only when cleanup() has been called the same number of times
# as initializeProcesses()
global _count
_count -= 1
if _count != 0:
return
if not six.PY2:
atexit.unregister(cleanup)
else:
try:
atexit._exithandlers.remove((cleanup, (), {}))
except ValueError:
pass
if neuroConfig.runsInfo:
neuroConfig.runsInfo.delete()
neuroConfig.clearObjects()
neuroHierarchy.databases.currentThreadCleanup()
brainvisa.processes.cleanupProcesses()
neuroLog.closeMainLog()
# print('closing manager:', temporary.manager, file=open('/tmp/log', 'a'))
sys.stdout.flush()
try:
temporary.manager.close()
# print('(set to None)', file=open('/tmp/log', 'a'))
except Exception as e:
print(e)
raise
sys.stdout.flush()
[docs]def initializeProcesses():
'''
This method intends to retrieve a list of all existing types in the
BrainVISA ontology, of all processes and databases. This replicates the
job which is usually done at the very beginning when BrainVISA starts,
but here no GUI is created.
The processes are available through functions in :py:mod:`brainvisa.processes`.
The databases are in :py:data:`brainvisa.data.neuroHierarchy.databases`.
The types are available through functions in :py:mod:`brainvisa.data.neuroDiskItems`.
'''
# protect agains recursive calls
global _count
_count += 1
if _count != 1:
return
atexit.register(cleanup)
if not neuroConfig.noToolBox:
brainvisa.toolboxes.readToolboxes(neuroConfig.toolboxesDir,
neuroConfig.homeBrainVISADir)
for toolbox in brainvisa.toolboxes.allToolboxes():
toolbox.init()
temporary.initializeTemporaryFiles(
defaultTemporaryDirectory=neuroConfig.temporaryDirectory)
initializeMinfExtensions()
if not neuroConfig.fastStart or neuroConfig.historyBookDirectory:
# check for expired run information : ask user what to do
if neuroConfig.fastStart:
dontrecordruns = True
else:
dontrecordruns = False
neuroConfig.runsInfo = neuroConfig.RunsInfo(
dontrecordruns=dontrecordruns)
neuroLog.initializeLog()
neuroData.initializeData()
neuroHierarchy.initializeDatabases()
brainvisa.processes.initializeProcesses()
if neuroConfig.gui:
from brainvisa.data.qtgui.neuroDataGUI import initializeDataGUI
initializeDataGUI()
from brainvisa.processing.qtgui.neuroProcessesGUI import initializeProcessesGUI
initializeProcessesGUI()
if not neuroConfig.fastStart:
# write information about brainvisa log file
brainvisa.processes.defaultContext().write(
"The log file for this session is " + repr(neuroConfig.logFileName))
neuroConfig.runsInfo.check(brainvisa.processes.defaultContext())
# brainvisa.processes.readTypes() (actually imported from neuroDiskItems)
# lists all existing types in the ontology
brainvisa.processes.readTypes()
# neuroHierarchy.databases gets populated
# Databases loading is skipped when no toolbox is loaded because specific
# hierarchies from unloaded toolboxes may be needed to define the ontology
# describing a given database organization
if not neuroConfig.noToolBox and not neuroConfig.fastStart:
neuroHierarchy.openDatabases()
# Makes the list of all processes availables in the processes path
brainvisa.processes.readProcesses(neuroConfig.processesPath)
if not neuroConfig.fastStart:
for toolbox in brainvisa.toolboxes.allToolboxes():
# executes startup.py of each toolbox if it exists
if os.path.exists(toolbox.startupFile):
try:
print('exec:', toolbox.startupFile)
with open(toolbox.startupFile, 'rb') as f:
code = compile(f.read(), f.name, 'exec')
six.exec_(code, globals(), {})
except Exception:
neuroException.showException()
localsStartup = {}
for f in neuroConfig.startup:
try:
if isinstance(f, six.string_types):
localsStartup = globals().copy()
code = compile(f, '<neuroConfig.startup>', 'exec')
six.exec_(code, localsStartup, localsStartup)
else:
f()
except Exception:
neuroException.showException()
del localsStartup
