# -*- coding: utf-8 -*-
# This software and supporting documentation are distributed by
# Institut Federatif de Recherche 49
# CEA/NeuroSpin, Batiment 145,
# 91191 Gif-sur-Yvette cedex
# France
#
# This software is governed by the CeCILL license version 2 under
# French law and abiding by the rules of distribution of free software.
# 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".
#
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
#
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
#
# 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.
"""
Several global variables are defined in this module to store **Brainvisa configuration and user options**:
.. py:data:: logFileName
path of Brainvisa log file where the history of the current session will be saved.
.. py:data:: platform
linux, windows...
.. py:data:: gui
false if Brainvisa is in batch mode
.. py:data:: sessionID
.. py:data:: fullVersion
shortVersion
Brainvisa version
.. py:data:: userProfile
if Brainvisa is started with ``-u`` option, the name of the profile stored in this variable is used to create a specific log file for this profile.
.. py:data:: siteOptionFile
path to a general options file that may be used for all users.
.. py:data:: userOptionFile
path to user options file.
.. py:data:: logFileName
path of Brainvisa log file where the history of the current session will be saved.
.. py:data:: runsInfo
information about the current executions of Brainvisa.
.. py:data:: temporaryDirectory
directory where temporary files will be written.
.. py:data:: mainPath
Path of Brainvisa main module.
.. py:data:: sharePath
Brainvisa share directory
.. py:data:: iconPath
.. py:data:: homeBrainVISADir
path to Brainvisa home directory (usually *$HOME/.brainvisa*)
.. py:data:: toolboxesDir
Brainvisa toolboxes directory
.. py:data:: processesPath
list of paths to Brainvisa processes (outside any toolbox)
.. py:data:: dataPath
list of DatabaseSettings objects indicating the selected databases.
.. py:data:: typesPath
list of paths to Brainvisa type files that contain the description of Brainvisa ontology.
.. py:data:: fileSystemOntologiesPath
list of paths to Brainvisa hierarchy files that contain the rules to organize Brainvisa databases directories.
.. py:data:: debugHierarchyScanning
stream where debug information about hierarchy rules may be written. Set with ``--debugHierarchy`` option.
.. py:data:: debugParameterLinks
stream where debug information about parameter links may be written. Set with `--debugLinks` option.
.. py:data:: sharedDatabaseFound
True if Brainvisa shared database which contain models, templates, referentials, etc, was found.
.. py:data:: mainDocPath
path to Brainvisa documentation directory
.. py:data:: docPath
path to Brainvisa documentation directory according to the choosen language.
.. py:data:: brainvisaSysEnv
:py:class:`soma.env.BrainvisaSystemEnv` - defines system environment variables that have to be passed to external command to restore environment if it have been modified at brainvisa startup
.. py:data:: ignoreValidation
Do not check vor invalid processes, all are enabled. Set with ``--ignoreValidation``.
.. py:data:: language
fr or en
.. py:data:: userLevel
the processes which level is greater than the user level are hidden. Basic = 0, advanced = 1, expert = 2.
.. py:data:: supportEmail
SMTP_server_name
.. py:data:: textEditor
.. py:data:: HTMLBrowser
.. py:data:: fastStart
if this mode is enabled, brainvisa starts faster but with less features. Set with ``-f`` or ``-r`` options.
.. py:data:: noToolBox
if enabled, Brainvisa toolboxes are not loaded. Set with ``--noToolBox``.
.. py:data:: setup
if enabled, the shared database is updated at startup. Set with ``--setup`` option.
.. py:data:: anatomistExecutable
anatomistImplementation
.. py:data:: matlabRelease
matlabExecutable
matlabOptions
matlabPath
matlabStartup
.. py:data:: spmDirectory
.. py:data:: Roptions
Rexecutable
.. py:data:: profileFileName
filename where profiling information may be written. Set with ``--profile`` option.
.. py:data:: historyBookDirectory
path to history_book directory, where processes executions and logs will be saved. Normally it is None so that it is stored in the database of each output data. But in some specific cases (distributed execution of single process) it can be useful to force it.
May be a list of directories: in that case, history files are duplicated in each of them.
"""
from __future__ import print_function
from __future__ import absolute_import
__docformat__ = 'restructuredtext en'
_defaultTranslateFunction = lambda x: x
import six.moves.builtins
if not hasattr(six.moves.builtins, '_t_'):
six.moves.builtins._t_ = _defaultTranslateFunction
import sys
import os
import errno
import re
import time
import socket
import tempfile
from soma.wip.application.api import Application
from brainvisa.configuration.api import initializeConfiguration, readConfiguration, DatabaseSettings
from soma.html import htmlEscape
from soma.uuid import Uuid
from soma.minf.api import readMinf, writeMinf
from soma.env import BrainvisaSystemEnv
import brainvisa
import six
import io
exitValue = 0
mainPath = os.path.normpath(
os.path.join(os.path.dirname(brainvisa.__file__), "..", "..", "brainvisa"))
sys.argv[0] = os.path.normpath(
os.path.abspath(os.path.join(mainPath, '..', 'bin', 'brainvisa')))
mainPath = os.path.normpath(os.path.abspath(mainPath))
if not os.path.isdir(mainPath):
raise RuntimeError('Cannot find main BrainVISA directory')
# Change sys.path[0] because Python follow symlinks when it adds
# this directory and we do not want that to be able to make symlinks
# in build tree to source tree and create the *.pyo or *.pyc in build tree.
basePath = os.path.dirname(mainPath)
sys.path[0:0] = [mainPath, os.path.join(basePath, 'python')]
# A bit of cleanup
sys.path = [os.path.normpath(os.path.abspath(p)) for p in sys.path]
_commandLine = " ".join(['"' + x + '"' for x in sys.argv])
def commandLine():
return _commandLine
platform = findPlatform()
if platform == 'windows':
pathSeparator = ';'
else:
pathSeparator = ':'
[docs]def findInPath(file,
pathlist=os.environ.get('PATH').split(pathSeparator),
is_dir=False):
"""Returns the directory containing file"""
for i in pathlist:
p = os.path.normpath(os.path.abspath(i))
if p:
if os.path.isdir(p) and os.path.exists(os.path.join(p, file)):
if (is_dir and os.path.isdir(os.path.join(p, file))) \
or (not is_dir and not os.path.isdir(os.path.join(p, file))):
return p
def executableWithPath(file,
pathlist=os.environ.get('PATH').split(pathSeparator)):
if os.path.isabs(file) and os.path.exists(file):
return file
path = findInPath(file, pathlist)
return os.path.join(path, file)
try:
from brainvisa.config import fullVersion, shortVersion
except ImportError:
f = os.path.join(mainPath, 'VERSION')
if not os.path.exists(f):
f = os.path.join(mainPath, '..', 'VERSION')
f = open(f)
fullVersion = f.readline()[:-1]
f.close()
shortVersion = '.'.join(fullVersion.split('.')[:2])
[docs]def versionNumber():
"""Returns Brainvisa short version X.Y as a float number"""
global shortVersion
return float(shortVersion)
[docs]def versionString():
"""Returns Brainvisa full version 'X.Y.Z'"""
global fullVersion
return fullVersion
[docs]def versionText():
"""Returns the text 'BrainVISA X.Y.Z'"""
return 'BrainVISA ' + versionString()
_sharePath = None
[docs]def getSharePath():
"""Returns BrainVISA share directory path."""
global _sharePath
if _sharePath is not None:
return _sharePath
try:
from soma.config import BRAINVISA_SHARE
_sharePath = BRAINVISA_SHARE
except ImportError:
path = os.getenv('PATH').split(os.pathsep)
for p in path:
if p.endswith('/bin') or p.endswith('\\bin'):
p = p[:len(p) - 4]
elif p.endswith( '/bin/commands-links' ) \
or p.endswith('\\bin\\commands-links'):
p = p[:len(p) - 19]
p = os.path.join(p, 'share')
if os.path.isdir(p):
_sharePath = p
break
if not _sharePath or \
(not os.path.isdir(os.path.join(_sharePath,
'axon-' + shortVersion))
and not os.path.isdir(os.path.join(_sharePath,
'brainvisa-' + shortVersion))):
# empty string rather than None to avoid later re-detection
_sharePath = ''
for projectName in ('axon', 'brainvisa'):
sharePath = os.path.normpath(os.path.join(mainPath, '..', 'share',
projectName + '-' + shortVersion))
if os.path.isdir(sharePath):
_sharePath = os.path.normpath(os.path.join(mainPath, '..',
'share'))
break
return _sharePath
[docs]def initializeOntologyPaths():
"""
Initializes the global variables :py:data:`typesPath` and :py:data:`fileSystemOntologiesPath`.
This function is used when toolboxes are reloaded.
"""
global typesPath
global fileSystemOntologiesPath
global mainPath
typesPath = [os.path.join(mainPath, 'types')]
fileSystemOntologiesPath = [os.path.join(mainPath, 'hierarchies')]
initializeOntologyPaths()
processesPath = [os.path.join(mainPath, 'processes')]
for projectName in ('axon', 'brainvisa'):
sharePath = os.path.join(getSharePath(), projectName + '-' + shortVersion)
if os.path.isdir(sharePath):
break
# Sources organization
sharePath = os.path.normpath(
os.path.join(mainPath, '..', 'share', projectName + '-' + shortVersion))
if os.path.isdir(sharePath):
break
iconPath = os.path.join(sharePath, 'icons')
uiPath = os.path.join(sharePath, 'ui')
toolboxesDir = os.path.join(mainPath, 'toolboxes')
# environment variable holding path for dynamic libraries
def libraryPathEnvironmentVariable():
if platform == 'windows':
return 'PATH'
elif platform == 'darwin':
return 'DYLD_LIBRARY_PATH'
return 'LD_LIBRARY_PATH'
# Define system environment variables that have to be passed to external
# command to restore environment if it have been modified at brainvisa
# startup
brainvisaSysEnv = BrainvisaSystemEnv()
# try to determine if we are in a build tree with system libraries - in that
# case, brainvisaSysEnv should not be altered when calling external commands
if not sys.executable.startswith(basePath):
# python is not in the BV tree, or it is a system-wide installation
brainvisaSysEnv.variables = {}
userLevel = 0
sessionID = Uuid()
temporaryDirectory = tempfile.gettempdir()
[docs]def getDocPath(path, project=''):
"""Returns the path of the documentation directory of the given project."""
# Language and documentation
result = os.path.join(getSharePath(), 'doc', project)
if not os.path.exists(result):
result = os.path.normpath(
os.path.join(path, '..', 'share', 'doc', project))
if not os.path.exists(result):
result = os.path.normpath(os.path.join(path, '..', 'doc'))
return result
docPath = mainDocPath = getDocPath(
mainPath, projectName + '-' + str(versionNumber()))
_languages = []
if os.path.exists(docPath):
for l in os.listdir(docPath):
if len(l) == 2 and os.path.isdir(os.path.join(mainDocPath, l)):
_languages.append(l)
else:
print(
'WARNING: You should check your BrainVISA installation because the following directory does not exist:',
repr(docPath), file=sys.stderr)
for i in ('LANGUAGE', 'LC_ALL', 'LC_MESSAGES', 'LANG'):
language = os.environ.get(i, '')[: 2]
if language in _languages:
break
if language not in _languages:
language = 'en'
# variable to ensure the format used for numbers
os.environ["LC_NUMERIC"] = "C"
# debug console defaults
shell = 0
# GUI defaults
gui = True
guiLoaded = False
qtApplication = None
# Create $HOME/.brainvisa directory
homedir = os.getenv('HOME')
if not homedir:
homedir = ''
if sys.platform[:3] == 'win':
homedir = os.getenv('USERPROFILE')
if not homedir:
homedir = os.getenv('HOMEPATH')
if not homedir:
homedir = '\\'
drive = os.getenv('HOMEDRIVE')
if not drive:
drive = os.getenv('SystemDrive')
if not drive:
drive = os.getenv('SystemRoot')
if not drive:
drive = os.getenv('windir')
if drive and len(drive) >= 2:
drive = drive[:2]
else:
drive = ''
homedir = drive + homedir
# Try to get BrainVISA user dir from environment variable
homeBrainVISADir = os.getenv('BRAINVISA_USER_DIR')
if not homeBrainVISADir:
# Uses default BrainVISA home directory
homeBrainVISADir = os.path.join(homedir, '.brainvisa')
if not os.path.exists(homeBrainVISADir):
if os.path.lexists(homeBrainVISADir):
# .brainvisa is a broken symbolic link, likely from
# /casa/home/.brainvisa to the host home directory; make the target
# directory
path_to_make = os.readlink(homeBrainVISADir)
else:
path_to_make = homeBrainVISADir
try:
os.mkdir(path_to_make)
except OSError as e:
if e.errno == errno.EEXIST:
# filter out 'File exists' exception, if the same dir has been
# created concurrently by another instance of BrainVisa or another
# thread
pass
else:
raise
# Other defaults
anatomistExecutable = 'anatomist'
anatomistImplementation = 'threaded'
remoteBrainvisaExecutable = ''
HTMLBrowser = ''
useHTMLBrowser = 0
matlabExecutable = 'matlab'
matlabRelease = None
matlabOptions = '-nosplash -nodisplay'
matlabPath = []
tmp = [os.path.join(homeBrainVISADir, 'matlab'),
os.path.join(mainPath, 'matlab')]
while tmp:
p = tmp.pop()
if os.path.isdir(p):
matlabPath.append(p)
for x in os.listdir(p):
tmp.append(os.path.join(p, x))
spmDirectory = ''
textEditor = ''
matlabStartup = []
dataPath = []
logFileName = None
cleanLog = False
profileFileName = ''
mainLog = None
brainvisaSessionLog = None
brainvisaSessionLogItem = None
startup = []
flatHierarchy = os.path.join(mainPath, 'shfjFlatHierarchy.py')
debugHierarchyScanning = None
debugParametersLinks = None
historyBookDirectory = None
userEmail = ''
supportEmail = 'support@brainvisa.info'
SMTP_server_name = 'localhost'
if platform == 'windows':
Rexecutable = 'Rterm.exe'
Roptions = '--no-restore --no-save --args'
else:
Rexecutable = 'R'
Roptions = '--vanilla --slave --args'
_openedDebugFiles = {
'-': sys.stdout,
'~': sys.stderr,
}
app = Application('brainvisa', versionString())
app.directories.user = homeBrainVISADir
app.directories.application = sharePath
[docs]def openDebugFile(fileName):
'''Opens a file to put debug messages in. If '-' is given, sys.stdout is
returned. If '~' is given, sys.stderr is returned. If this function is
used several times with the same fileName, the same file object is retured.
'''
result = _openedDebugFiles.get(fileName)
if result is None:
result = open(fileName, 'a')
_openedDebugFiles[fileName] = result
return result
#------------------------------------------------------------------------------
[docs]def chooseDatabaseVersionSyncOption(context):
"""
Asks user to choose a database synchronization mode (Automatic or manual) when a database is used with different versions of Brainvisa.
The choice is saved in brainvisa options file.
:param context: The context enables to adapt the interaction with the user according to Brainvisa mode of execution (graphical, batch)
:returns: the user choice: *auto* for automatic mode, *man* for manual mode.
"""
global databaseVersionSync, userOptionFile
choice = context.ask(
"<p><b>Database synchronization between different versions of BrainVISA<b></p><p>Some of your databases have been used with different versions of BrainVISA. They may need to be updated when you switch from one BrainVISA version to another.</p> Please choose the way you want to manage the database synchronization throught BrainVISA versions : <ul><li>Automatic (recommended) : BrainVISA will automatically update your database if you switch from one BrainVISA version to another. </li><li>Manual : Database update is not automatic when switch from one BrainVISA version to another but if you modify a database in one version, you will have to update it with the other version for BrainVISA to take into account the modifications.</li></ul><p>You can change this option later in BrainVISA preferences.</p>", "Automatic (recommended)", "Manual")
if (choice == 0):
databaseVersionSync = "auto"
else:
databaseVersionSync = "man"
app = Application()
app.configuration.brainvisa.databaseVersionSync = databaseVersionSync
app.configuration.save(userOptionFile)
return databaseVersionSync
[docs]def stdinLoop():
"""
Reads Brainvisa commands on stdin and executes them.
"""
e = []
for l in sys.stdin:
if l.startswith('# brainvisa run commands'):
exec(''.join(e))
e = []
else:
e.append(l)
if e:
exec(''.join(e))
# Parse command Line
# To use -- <Other options> do not use sys.argv but args (returned by getopt)
userProfile = None
openMainWindow = 1
showHelp = 0
fastStart = False
global setup
setup = False
noToolBox = False
ignoreValidation = False
def convertCommandLineParameter(i):
if len(i) > 0 and (i[0] in '[({' or i in ('None', 'True', 'False')):
try:
res = eval(i)
except Exception:
res = i
else:
res = i
return res
try:
i = sys.argv.index('-r')
except ValueError:
i = -1
if i >= 0:
gui = 0
fastStart = True
# noToolBox = True
logFileName = ''
startup.append('defaultContext().runProcess' + repr(
tuple((convertCommandLineParameter(i) for i in sys.argv[i + 1:]))))
else:
import getopt
# Ignore Qt -style attribute
try:
i = sys.argv.index('-style')
argv = sys.argv[1:i] + sys.argv[i + 2:]
except ValueError:
argv = sys.argv[1:]
try:
opts, args = getopt.getopt(argv, "bfe:c:s:u:h",
["updateDocumentation", "noMainWindow",
"logFile=", "cleanLog", "profile=", "shell",
"debugHierarchy=", "debugLinks=",
"help", "setup", "noToolBox",
"ignoreValidation"])
except getopt.GetoptError as msg:
# print help information and exit:
sys.stderr.write(
"error in options: %s\nUse -h or --help for help\n" % msg)
sys.exit(1)
for o, a in opts:
if o in ("-b", ):
gui = 0
elif o in ("-e", ):
if a == '-':
startup.append('neuroConfig.stdinLoop()')
else:
startup.append("with open({0!r}, 'rb') as f:\n"
" code = compile(f.read(), {0!r}, 'exec')\n"
"six.exec_(code)\n"
.format(a))
elif o in ("-c", ):
startup.append(a)
elif o in ("-s", ):
m = re.match(r'(.*)\((.*[^)])\)?', a)
if m:
startup.append(
'brainvisa.processing.qt4gui.neuroProcessesGUI.showProcess("' + m.group(1) + '",' + m.group(2) + ')')
else:
startup.append(
'brainvisa.processing.qt4gui.neuroProcessesGUI.showProcess("' + a + '")')
elif o in ("-u", ):
userProfile = a
elif o in ("-f", ):
fastStart = True
elif o in ("--updateDocumentation", ):
startup.append('generateHTMLProcessesDocumentation()')
elif o in ("--noMainWindow", ):
openMainWindow = 0
elif o in ("--logFile", ):
logFileName = a
elif o in ("--cleanLog",):
cleanLog = True
elif o in ("--profile", ):
profileFileName = a
elif o in ("--shell", ):
shell = 1
elif o in ("--debugHierarchy", ):
debugHierarchyScanning = openDebugFile(a)
elif o in ("--debugLinks", ):
debugParametersLinks = openDebugFile(a)
elif o in ("-h", "--help"):
showHelp = 1
elif o in ("--setup"):
setup = True
elif o in ("--noToolBox"):
noToolBox = True
elif o in ("--ignoreValidation"):
ignoreValidation = True
# Print(help)
if showHelp == 1:
print('''
Usage: brainvisa [ <BrainVISA options> ] [ -- <other options> ]
<BrainVISA options> are interpreted by BrainVISA, <other options> are
passed to BrainVISA scripts (technically, they are kept in sys.argv).
BrainVISA options:
-b Run in batch mode: no graphical interface started by BrainVISA.
-e <file> Execute <file> which must be a valid Python script.
-c <command> Execute <command> which must be a valid Python command.
--shell Run BrainVISA in a IPython shell, if IPython is
available (see http://ipython.scipy.org).
-s <process_id> Open a process window. Equivalent to -c 'brainvisa.processing.qt4gui.neuroProcessesGUI.showProcess("<process_id>")'.
-u <profile> Select a user profile.
--logFile <file> Change the log file name (default=$HOME/.brainvisa/brainvisa.log).
--updateDocumentation Generate processes and types HTML documentation pages.
--setup Update the shared database at startup.
--noMainWindow Do not open Brainvisa main window.
--noToolBox Do not load any process nor toolbox.
--cleanLog Clean home brainvisa directory by removing session information (current_runs.minf) and all log files (brainvisa*.log)
--ignoreValidation Do not check vor invalid processes, all are enabled.
(generally not useful)
-f Run in faststart mode: databases are not loaded, processes are loaded from a cache
(this mode is used when processes are run in parallel via Soma-workflow).
--debugHierarchy <file> Write ontology rules debug information in <file>.
--debugLinks <file> Write parameter links debug information in <file>.
-r <process specs> Run a process in batch mode, and quit after execution.
The process specs can be either a .bvproc filename,
or a process name followed by its paremeters.
Parameters names cannot be specified in arguments,
so they must be provided in the correct order:
brainvisa -r process.bvproc
brainvisa -r threshold ~/data/irm.ima /tmp/th.nii "greater than" 80
This used to be the standard way to run batches, but
now it is recommended to use
"python -m brainvisa.axon.runprocess",
which is lighter, instead, and more flexible on
parameters (parameters names are allowed).
-h or --help Show help message in batch mode and exit.
Notes:
Multiple -e and -c commands are executed in the order they are given after
all initialization steps are done (options parsing, databases and processes
parsing, etc.).
''')
sys.exit()
if setup:
startup.append(
'from brainvisa.data.neuroHierarchy import databases\nfrom brainvisa.processes import defaultContext\ndb = list( databases.iterDatabases() )[0]\ndb.clear(context=defaultContext())\ndb.update(context=defaultContext())')
#
[docs]class RunsInfo(object):
"""
This class gets information about possibly existing runs of Brainvisa and adds information about the current one.
:var string file: information about current runs is stored in *<Brainvisa home dir>/current_runs.minf*
:var integer currentRun: index of the current execution of Brainvisa (from 1)
:var float timeout: timeout before asking the user if the execution of Brainvisa is still alive. When Brainvisa fails, the file current_runs.minf may not be cleaned.
:var dictionary runs: information about current executions of Brainvisa. The information is loaded from the minf file and information about the current execution is added. It is a dictionary *{index -> {host, pid, time, logFileName} }*
:var integer count: number of executions of Brainvisa
:var dictonary expiredRuns: dictionary containing the runs for which the timeout is reached. The user will be asked if these runs are still alive. If not, the corresponding log files will be deleted and the *current_runs.minf* file will be cleaned.
"""
def __init__(self, dontrecordruns=False):
global logFileName
global cleanLog
self.dontrecordruns = dontrecordruns
if dontrecordruns:
fd, self.file = tempfile.mkstemp(suffix='.minf',
prefix='bv_current_runs', dir=temporaryDirectory, text=True)
os.close(fd)
os.unlink(self.file)
else:
self.file = os.path.join(homeBrainVISADir, "current_runs.minf")
if cleanLog:
try:
if os.path.exists(self.file):
os.remove(self.file)
for f in os.listdir(homeBrainVISADir):
if f.startswith("brainvisa") and (f.endswith(".log") or f.endswith(".log~")):
os.remove(os.path.join(homeBrainVISADir, f))
except Exception as e:
print("Fail cleaning log files:")
print(e)
self.currentRun = 1
self.timeout = 604800 # 7 days in seconds
self.runs = {}
self.count = 0
self.expiredRuns = {}
try:
if os.path.exists(self.file):
self.runs, self.count = readMinf(self.file)
currentTime = time.time()
# register information for current run
infos = {
'host': socket.gethostname(), 'pid': os.getpid(), 'time': currentTime}
self.count += 1
i = 1
while ((i <= self.count + 1) and i in self.runs):
i += 1
self.currentRun = i
if logFileName is None:
if dontrecordruns:
fd, logFileName = tempfile.mkstemp(
suffix='.log', prefix='brainvisa',
dir=temporaryDirectory, text=True)
os.close(fd)
os.unlink(logFileName)
elif self.currentRun > 1:
logFileName = os.path.join(
homeBrainVISADir, 'brainvisa' + str(self.currentRun) + '.log')
else:
logFileName = os.path.join(
homeBrainVISADir, 'brainvisa.log')
else:
self.currentRun = logFileName
infos["logFileName"] = logFileName
self.runs[self.currentRun] = infos
self.write()
except Exception as e:
print("Fail to get or set current runs information:")
print(e)
if os.path.exists(self.file):
os.remove(self.file)
[docs] def delete(self):
"""
Removes current run information from the current_runs.minf file.
"""
if os.path.exists(self.file):
try:
if self.dontrecordruns:
os.unlink(self.file)
else:
self.runs, self.count = readMinf(self.file)
self.runs.pop(self.currentRun, None)
self.count = len(self.runs)
self.write()
except Exception:
pass
[docs] def check(self, context):
"""
Checks if there are expired runs and asks the user what to do.
"""
if self.dontrecordruns:
return # don't check in this mode
if os.path.exists(self.file):
try:
self.runs, self.count = readMinf(self.file)
except Exception as e:
print('Cannot read "' + self.file + '":', file=sys.stderr)
print(e, file=sys.stderr)
return
currentTime = time.time()
# check for expired runs
for n, run in self.runs.items():
if currentTime - run["time"] > self.timeout:
self.expiredRuns[n] = run
if self.expiredRuns:
choice = 0
if gui: # ask user if brainvisa is not started in batch mode
message = "The following Brainvisa sessions have expired. Maybe they terminated abnormally : \n"
for n, run in self.expiredRuns.items():
logfile = run.get("logFileName", os.path.join(
homeBrainVISADir, 'brainvisa' + str(n) + '.log'))
run["logFileName"] = logfile
message += "\t- Brainvisa process " + str(run["pid"]) + " on machine " + str(
run["host"]) + " started at " + time.ctime(run["time"]) + " - log file : " + logfile + "\n"
message += "\nAre these processes still running?\nIf no, sessions information and associated log file will be deleted.\nif yes, the timeout will be increased."
currentTime = time.time()
choice = context.ask(message, "No", "Yes")
if choice == 1: # the processes are still running
for n in self.expiredRuns.keys():
self.runs[n]["time"] = currentTime
else:
for n in self.expiredRuns.keys():
logfile = self.expiredRuns[n].get("logFileName", None)
if logfile is not None and os.path.exists(logfile):
try:
os.remove(logfile)
if os.path.exists(logfile + "~"):
os.remove(logfile + "~")
except Exception as e:
print(e)
print("Fail removing log file.")
del self.runs[n]
self.count = len(self.runs)
self.write()
def write(self):
writeMinf(self.file, (self.runs, self.count,))
# Set log file name
if logFileName is None:
if userProfile:
logFileName = os.path.join(
homeBrainVISADir, 'brainvisa-' + userProfile + '.log')
runsInfo = None
initializeConfiguration()
# add brainvisa shared database to the list of available databases
sharedDatabaseFound = False
try:
import brainvisa_share.config
bvShareDirectory = brainvisa_share.config.share
except Exception:
bvShareDirectory = 'brainvisa-share-' + shortVersion
for p in (os.path.join(getSharePath(), bvShareDirectory),
os.path.join(getSharePath(), 'shfj-' + shortVersion),
os.path.join(getSharePath(), 'shfj')):
if os.path.isdir(p):
dataPath.insert(0, DatabaseSettings(p, read_only=True))
dataPath[0].builtin = True # mark as a builtin, non-removable database
sharedDatabaseFound = True
break
class Translator(object):
def __init__(self, lang=language):
self.language = lang
self.translations = self.getTranslations()
def translate(self, msg):
return self.translations.get(msg, msg)
def getTranslations(self):
translations = dict()
for filePath in self.getTranslationFiles():
file = io.open(filePath, 'r', encoding='utf-8')
translations.update(readMinf(file)[0])
file.close()
return translations
def getTranslationFiles(self):
baseDocPath = getDocPath(mainPath)
for directory in os.listdir(baseDocPath):
file = os.path.join(
baseDocPath, directory, self.language, 'translation.minf')
if os.path.exists(file):
yield file
def initGlobalVariables():
global mainPath, userProfile, homeBrainVISADir
for attr, value in readConfiguration(mainPath, userProfile, homeBrainVISADir):
if isinstance(value, list):
globals()[attr] += value
else:
globals()[attr] = value
# Clean pathes
global typesPath, dataPath, processesPath, fileSystemOntologiesPath, matlabPath
for p in (typesPath, dataPath, processesPath, fileSystemOntologiesPath, matlabPath):
i = 0
l = []
while i < len(p):
if p[i] in l:
del p[i]
else:
l.append(p[i])
i += 1
# Translations
global docPath, language, _defaultTranslateFunction
os.environ['LANGUAGE'] = language
docPath = os.path.join(docPath, language)
if _t_ is _defaultTranslateFunction:
try:
six.moves.builtins.__dict__['_t_'] = Translator(language).translate
except Exception as msg:
six.moves.builtins.__dict__['_t_'] = lambda x: x
sys.stderr.write(str(msg) + '\n')
def get_database_settings(name, selected=True, read_only=False):
global dataPath
for dbs in dataPath:
if dbs.directory == name:
return dbs
# not found, create a new one
return DatabaseSettings(name, selected=selected, read_only=read_only)
[docs]def getDocFile(filename):
"""
Search doc file in doc path and if not found, in english documentation path.
"""
global docPath, mainDocPath
path = os.path.join(docPath, filename)
if not os.path.exists(path):
path = os.path.join(mainDocPath, "en", filename)
return path
# Pathes for binaries and libraries
# (shouldn't we just test platform != 'windows' ?) (Denis)
# if platform != 'windows':
# if 'PATH' in os.environ:
# os.environ[ 'PATH' ] = os.path.join( mainPath, 'bin', platform ) + ':' + os.path.join( mainPath, 'bin' ) + ':' + \
# os.environ[ 'PATH' ]
# else:
# os.environ[ 'PATH' ] = os.path.join( mainPath, 'bin', platform ) + ':' + os.path.join( mainPath, 'bin' )
# libpathenv = libraryPathEnvironmentVariable()
# if libpathenv in os.environ:
# os.environ[ libpathenv ] = \
# os.path.join( mainPath, 'lib', platform ) + ':' + \
# os.environ[ libpathenv ]
# else:
# os.environ[ libpathenv ] = os.path.join( mainPath, 'lib', platform )
# Setup GUI
_allObjects = {}
def registerObject(object):
global _allObjects
_allObjects[object] = object
def unregisterObject(object):
global _allObjects
try:
del _allObjects[object]
return True
except Exception:
return False
def clearObjects():
global _allObjects
_allObjects = {}
[docs]def environmentHTML():
"""
Returns an HTML page displaying Brainvisa configuration:
* Brainvisa version
* Python Version
* Command line used to start Brainvisa
* Environment variables
* Brainvisa options (global variables of this module)
This page is displayed in Brainvisa log in starting Brainvisa item.
"""
from brainvisa.toolboxes import allToolboxes
content = '<html><body><h1>' + htmlEscape( versionText() ) + '''</h1>
<h2>''' + _t_( 'Python version' ) + '</h2>' + htmlEscape( sys.version ) + '''
<h2>''' + _t_( 'Command line' ) + '''</h2>
<tt>''' + htmlEscape( commandLine() ) + '''</tt>
<h2>''' + _t_( 'Toolboxes' ) + '</h2>\n' + \
'\n'.join((i.name + '<br>' for i in allToolboxes()))
content += '<h2>' + _t_('Environment variables') + '</h2>'
for n, v in os.environ.items():
content += '<tt><em>' + n + '</em> = ' + htmlEscape(v) + '</tt><p>'
content += '<h2>' + _t_('BrainVISA options') + '</h2>'
g = globals()
for n in ('platform', 'gui', 'sessionID', 'userProfile', 'siteOptionFile',
'userOptionFile',
'logFileName', 'temporaryDirectory', 'mainPath', 'iconPath',
'typesPath', 'dataPath', 'processesPath', 'fileSystemOntologiesPath',
'mainDocPath', 'docPath',
'anatomistExecutable', 'matlabRelease', 'matlabExecutable',
'matlabOptions', 'matlabPath',
#'matlabLibraryDirectory',
'matlabStartup', 'spmDirectory',
'logFileName', 'language', 'userLevel',
'startup', 'supportEmail', 'SMTP_server_name', 'flatHierarchy',
'textEditor'):
content += '<code><em>' + n + '</em> = ' + \
htmlEscape(str(g[n])) + '</code><p>'
content += '</body></html>'
return content
