# -*- 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.
'''
@author: Yann Cointepas
@organization: U{NeuroSpin<http://www.neurospin.org>} and U{IFR 49<http://www.ifr49.org>}
@license: U{CeCILL version 2<http://www.cecill.info/licences/Licence_CeCILL_V2-en.html>}
'''
__docformat__ = "epytext en"
import sys, os, time
from soma.wip.application.api import Application
from brainvisa.configuration.brainvisa_configuration import BrainVISAConfiguration
from brainvisa.configuration.databases_configuration import DatabasesConfiguration, DatabaseSettings
from brainvisa.configuration.anatomist_configuration import AnatomistConfiguration
from brainvisa.configuration.r_configuration import RConfiguration
from brainvisa.configuration.matlab_configuration import MatlabConfiguration
from brainvisa.configuration.spm_configuration import SPMConfiguration
from brainvisa.configuration.fsl_configuration import FSLConfiguration
try :
from brainvisa.configuration.datastorage_configuration import DataStorageConfiguration
except Exception, e :
pass
from soma.configuration import Configuration
from soma.translation import translate as _
from brainvisa import shelltools
#------------------------------------------------------------------------------
def initializeConfiguration():
configuration = Application().configuration
configuration.add( 'brainvisa', BrainVISAConfiguration() )
configuration.add( 'databases', DatabasesConfiguration() )
configuration.add( 'anatomist', AnatomistConfiguration() )
configuration.add( 'R', RConfiguration() )
configuration.add( 'matlab', MatlabConfiguration() )
configuration.add( 'SPM', SPMConfiguration() )
configuration.add( 'FSL', FSLConfiguration() )
try :
configuration.add( 'datastorage', DataStorageConfiguration() )
except Exception, e :
pass
#------------------------------------------------------------------------------
def readConfiguration( mainPath, userProfile, homeBrainVISADir ):
from brainvisa.processing.neuroException import showException
configuration = Application().configuration
siteOptionFile = os.path.join( mainPath, 'options.minf' )
siteStartupFile = os.path.join( mainPath, 'startup.py' )
if os.path.exists( siteOptionFile ):
exceptions=configuration.load( siteOptionFile )
for exc in exceptions:
showException(beforeError="Error while reading options from "+siteOptionFile+"<br>", afterError="<br>The option will be ignored.", exceptionInfo=exc)
else:
oldSiteOptionFile = siteOptionFile[ :-4 ] + 'py'
if os.path.exists( oldSiteOptionFile ):
convertConfiguration30To31( oldSiteOptionFile, siteOptionFile,
siteStartupFile )
if os.path.exists( siteStartupFile ):
exceptions=configuration.load( siteStartupFile )
for exc in exceptions:
showException(beforeError="Error while reading options from "+siteStartupFile+"<br>", afterError="<br>The option will be ignored.", exceptionInfo=exc)
if userProfile is None:
userOptionFile = os.path.join( homeBrainVISADir, 'options.minf' )
userStartupFile = os.path.join( os.path.dirname( userOptionFile ),
'startup.py' )
if not os.path.exists( userOptionFile ):
oldUserOptionFile = userOptionFile[ :-4 ] + 'py'
if os.path.exists( oldUserOptionFile ):
convertConfiguration30To31( oldUserOptionFile, userOptionFile,
userStartupFile )
else:
userOptionFile = os.path.join( homeBrainVISADir, 'options-' \
+ userProfile + '.minf' )
userStartupFile = os.path.join( homeBrainVISADir, 'startup-' \
+ userProfile + '.py' )
if not os.path.exists( userOptionFile ):
oldUserOptionFile = userOptionFile[ :-4 ] + 'py'
if os.path.exists( oldUserOptionFile ):
userStartupFile = os.path.join( homeBrainVISADir, 'startup-' \
+ userProfile + '.minf' )
convertConfiguration30To31( oldUserOptionFile, userOptionFile,
userStartupFile )
if not os.path.exists( userOptionFile ):
commonUserOptionFile = os.path.join( homeBrainVISADir, 'options.minf' )
commonUserStartupFile = os.path.join( homeBrainVISADir, 'startup.py' )
if not os.path.exists( commonUserOptionFile ):
oldUserOptionFile = commonUserOptionFile[ :-4 ] + 'py'
if os.path.exists( oldUserOptionFile ):
convertConfiguration30To31( oldUserOptionFile, commonUserOptionFile,
commonUserStartupFile )
if os.path.exists( commonUserOptionFile ):
shelltools.cp( commonUserOptionFile, userOptionFile )
if os.path.exists( commonUserStartupFile ):
shelltools.cp( commonUserStartupFile, userStartupFile )
if os.path.exists( userOptionFile ):
exceptions=configuration.load( userOptionFile )
for exc in exceptions:
showException(beforeError="Error while reading options from "+userOptionFile+"<br>", afterError="<br>The option will be ignored.", exceptionInfo=exc)
equiv31_30 = {
'R.executable': 'Rexecutable',
'R.options': 'Roptions',
'anatomist.executable': 'anatomistExecutable',
'brainvisa.htmlBrowser': 'HTMLBrowser',
'brainvisa.language': 'language',
'brainvisa.processesPath': 'processesPath',
'brainvisa.removeTemporary': 'removeTemporary',
'brainvisa.support.smtpServer': 'SMTP_server_name',
'brainvisa.support.supportEmail': 'supportEmail',
'brainvisa.support.userEmail': 'userEmail',
'brainvisa.temporaryDirectory': 'temporaryDirectory',
'brainvisa.textEditor': 'textEditor',
'brainvisa.userLevel': 'userLevel',
'matlab.executable': 'matlabExecutable',
'matlab.options': 'matlabOptions',
'matlab.path': 'matlabPath',
'matlab.startup': 'matlabStartup',
'matlab.version': 'matlabRelease'
}
yield ( 'siteOptionFile', siteOptionFile )
yield ( 'userOptionFile', userOptionFile )
yield ( 'siteStartupFile', siteStartupFile )
yield ( 'userStartupFile', userStartupFile )
for newKey, oldKey in equiv31_30.iteritems():
value = configuration
for attr in newKey.split( '.' ):
value = getattr( value, attr )
if value:
yield ( oldKey, value )
setSPM99Compatibility( configuration.brainvisa.SPM )
newDataPath = []
for fso in configuration.databases.fso:
if fso.selected:
newDataPath.append( DatabaseSettings( fso.directory ) )
yield ( 'dataPath', newDataPath )
yield ( 'databasesWarning', configuration.brainvisa.databasesWarning)
yield ( 'databaseVersionSync', configuration.brainvisa.databaseVersionSync )
#------------------------------------------------------------------------------
def convertConfiguration30To31( sourceFileName, destFileName,
startupfileName ):
class Options3_0:
equiv30_31 = {
'showSplashScreen': None,
'userLevel': 'brainvisa.userLevel',
'language': 'brainvisa.language',
'processesPath': 'brainvisa.processesPath',
'fileSystemOntologiesPath': None,
'startup': None,
'temporaryDirectory': 'brainvisa.temporaryDirectory',
'anatomistExecutable': 'anatomist.executable',
'matlabRelease': 'matlab.version',
'matlabExecutable': 'matlab.executable',
'matlabOptions': 'matlab.options',
'matlabPath': 'matlab.path',
'matlabStartup': 'matlab.startup',
'Rexecutable': 'R.executable',
'Roptions': 'R.options',
'spmDirectory': None,
'textEditor': 'brainvisa.textEditor',
'useHTMLBrowser': None,
'HTMLBrowser': 'brainvisa.htmlBrowser',
'removeTemporary': 'brainvisa.removeTemporary',
'multiconvExecutable': None,
'dataHandlerExecutable': None,
'userEmail': 'brainvisa.support.userEmail',
'supportEmail': 'brainvisa.support.supportEmail',
'SMTP_server_name': 'brainvisa.support.smtpServer',
}
def __init__( self, configuration ):
self.configuration = configuration
def set( self, name, value ):
dest = self.equiv30_31.get( name )
if dest is not None:
dest = dest.split( '.' )
obj = self.configuration
for attr in dest[:-1]:
obj = getattr( obj, attr )
setattr( obj, dest[ -1 ], obj.signature[ dest[-1] ].type.convertAttribute( obj, dest[ -1 ], value ) )
def addDatabaseDirectory( self, directory, hierarchy=None, selected=True ):
self.configuration.databases.fso.append( DatabasesConfiguration.FileSystemOntology( directory, selected ) ) #DatabasesConfiguration.FileSystemOntology( directory, hierarchy, selected ) )
def append( self, name, value ):
dest = self.equiv30_31.get( name )
if dest is not None:
dest = dest.split( '.' )
obj = self.configuration
for attr in dest[:-1]:
obj = getattr( obj, attr )
getattr( obj, dest[ -1 ] ).append( value )
def convertStartupCode30to31( fileName, outFileName ):
if os.path.exists( outFileName ):
return # already done or manually converted
beforeOptions = ''
afterOptions = ''
if os.path.exists( fileName ):
file = open( fileName )
location = 0
for line in file.xreadlines():
if location == 0:
if line == '#------------- DO NOT CHANGE ANYTHING BELOW (INCLUDING THIS LINE) -------------\n':
location = 1
else:
beforeOptions += line
elif location == 1:
if line == '#------------- DO NOT CHANGE ANYTHING ABOVE (INCLUDING THIS LINE) -------------\n':
location = 2
else:
afterOptions += line
file.close()
if beforeOptions or afterOptions:
file = open( outFileName, 'w' )
file.write( '#------------- BrainVISA startup code file -------------'
'\n' )
file.write( '#--- automatically converted from 3.0 (options.py) to '
'3.1\n' )
file.write( '#--- conversion date: ' + time.asctime() + '\n\n' )
if beforeOptions:
file.write( '#--- code used to be done before the automatic part of '
'options.py\n' )
file.write( beforeOptions )
if afterOptions:
file.write( '\n#--- code done after standard options\n' )
file.write( afterOptions )
configuration = Configuration()
configuration.add( 'brainvisa', BrainVISAConfiguration() )
configuration.add( 'databases', DatabasesConfiguration() )
configuration.add( 'anatomist', AnatomistConfiguration() )
configuration.add( 'R', RConfiguration() )
configuration.add( 'matlab', MatlabConfiguration() )
from brainvisa.configuration.neuroConfig import versionNumber
d = { 'options': Options3_0( configuration ), 'versionNumber': versionNumber }
try:
execfile( sourceFileName, d, d )
except:
import traceback
print >> sys.stderr, _( 'Cannot execute "%s":' % sourceFileName )
traceback.print_exc()
return
try:
configuration.save( destFileName )
except:
print >> sys.stderr, _( 'Cannot convert "%(old)s" to "%(new)s"' % {
'old': sourceFileName, 'new': destFileName } )
#raise
convertStartupCode30to31( sourceFileName, startupfileName )
#------------------------------------------------------------------------------
def setSPM99Compatibility( values ):
from brainvisa.configuration import neuroConfig
aimsrc = os.path.join( neuroConfig.homedir, '.aimsrc' )
if values.SPM99_compatibility or ( not values.radiological_orientation ) or os.path.exists( aimsrc ):
aimsrc = open( aimsrc, 'w' )
print >> aimsrc, "attributes = {\n '__syntax__' : 'aims_settings',"
if values.SPM99_compatibility:
print >> aimsrc, " 'spm_input_spm2_normalization' : 0,\n" \
" 'spm_output_spm2_normalization' : 0,\n" \
" 'spm_output_4d_volumes' : 0,\n" \
" 'nifti_output_4d_volumes' : 0,"
else:
print >> aimsrc, " 'spm_input_spm2_normalization' : 1,\n" \
" 'spm_output_spm2_normalization' : 1,\n" \
" 'spm_output_4d_volumes' : 1,\n" \
" 'nifti_output_4d_volumes' : 1,"
if values.radiological_orientation:
print >> aimsrc, " 'spm_input_radio_convention' : 1,\n" \
" 'spm_output_radio_convention' : 1,"
else:
print >> aimsrc, " 'spm_input_radio_convention' : 0,\n" \
" 'spm_output_radio_convention' : 0,"
print >> aimsrc, "}"
aimsrc.close()