brainvisa configuration modules¶
brainvisa.configuration.api¶
@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>}
brainvisa.configuration.neuroConfig¶
Several global variables are defined in this module to store Brainvisa configuration and user options:
- brainvisa.configuration.neuroConfig.logFileName¶
path of Brainvisa log file where the history of the current session will be saved.
- brainvisa.configuration.neuroConfig.platform¶
linux, windows…
- brainvisa.configuration.neuroConfig.gui¶
false if Brainvisa is in batch mode
- brainvisa.configuration.neuroConfig.sessionID¶
- brainvisa.configuration.neuroConfig.fullVersion¶
- brainvisa.configuration.neuroConfig.shortVersion¶
Brainvisa version
- brainvisa.configuration.neuroConfig.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.
- brainvisa.configuration.neuroConfig.siteOptionFile¶
path to a general options file that may be used for all users.
- brainvisa.configuration.neuroConfig.userOptionFile¶
path to user options file.
- brainvisa.configuration.neuroConfig.logFileName¶
path of Brainvisa log file where the history of the current session will be saved.
- brainvisa.configuration.neuroConfig.runsInfo¶
information about the current executions of Brainvisa.
- brainvisa.configuration.neuroConfig.temporaryDirectory¶
directory where temporary files will be written.
- brainvisa.configuration.neuroConfig.mainPath¶
Path of Brainvisa main module.
Brainvisa share directory
- brainvisa.configuration.neuroConfig.iconPath¶
- brainvisa.configuration.neuroConfig.homeBrainVISADir¶
path to Brainvisa home directory (usually $HOME/.brainvisa)
- brainvisa.configuration.neuroConfig.toolboxesDir¶
Brainvisa toolboxes directory
- brainvisa.configuration.neuroConfig.processesPath¶
list of paths to Brainvisa processes (outside any toolbox)
- brainvisa.configuration.neuroConfig.dataPath¶
list of DatabaseSettings objects indicating the selected databases.
- brainvisa.configuration.neuroConfig.typesPath¶
list of paths to Brainvisa type files that contain the description of Brainvisa ontology.
- brainvisa.configuration.neuroConfig.fileSystemOntologiesPath¶
list of paths to Brainvisa hierarchy files that contain the rules to organize Brainvisa databases directories.
- brainvisa.configuration.neuroConfig.debugHierarchyScanning¶
stream where debug information about hierarchy rules may be written. Set with
--debugHierarchy
option.
- brainvisa.configuration.neuroConfig.debugParameterLinks¶
stream where debug information about parameter links may be written. Set with –debugLinks option.
True if Brainvisa shared database which contain models, templates, referentials, etc, was found.
- brainvisa.configuration.neuroConfig.mainDocPath¶
path to Brainvisa documentation directory
- brainvisa.configuration.neuroConfig.docPath¶
path to Brainvisa documentation directory according to the choosen language.
- brainvisa.configuration.neuroConfig.brainvisaSysEnv¶
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
- brainvisa.configuration.neuroConfig.ignoreValidation¶
Do not check vor invalid processes, all are enabled. Set with
--ignoreValidation
.
- brainvisa.configuration.neuroConfig.language¶
fr or en
- brainvisa.configuration.neuroConfig.userLevel¶
the processes which level is greater than the user level are hidden. Basic = 0, advanced = 1, expert = 2.
- brainvisa.configuration.neuroConfig.supportEmail¶
- brainvisa.configuration.neuroConfig.SMTP_server_name¶
- brainvisa.configuration.neuroConfig.textEditor¶
- brainvisa.configuration.neuroConfig.HTMLBrowser¶
- brainvisa.configuration.neuroConfig.fastStart¶
if this mode is enabled, brainvisa starts faster but with less features. Set with
-f
or-r
options.
- brainvisa.configuration.neuroConfig.noToolBox¶
if enabled, Brainvisa toolboxes are not loaded. Set with
--noToolBox
.
- brainvisa.configuration.neuroConfig.setup¶
if enabled, the shared database is updated at startup. Set with
--setup
option.
- brainvisa.configuration.neuroConfig.anatomistExecutable¶
- brainvisa.configuration.neuroConfig.anatomistImplementation¶
- brainvisa.configuration.neuroConfig.matlabRelease¶
- brainvisa.configuration.neuroConfig.matlabExecutable¶
- brainvisa.configuration.neuroConfig.matlabOptions¶
- brainvisa.configuration.neuroConfig.matlabPath¶
- brainvisa.configuration.neuroConfig.matlabStartup¶
- brainvisa.configuration.neuroConfig.spmDirectory¶
- brainvisa.configuration.neuroConfig.profileFileName¶
filename where profiling information may be written. Set with
--profile
option.
- brainvisa.configuration.neuroConfig.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.
- class brainvisa.configuration.neuroConfig.RunsInfo(dontrecordruns=False)[source]¶
Bases:
object
This class gets information about possibly existing runs of Brainvisa and adds information about the current one.
- Variables
file (string) – information about current runs is stored in <Brainvisa home dir>/current_runs.minf
currentRun (integer) – index of the current execution of Brainvisa (from 1)
timeout (float) – 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.
runs (dictionary) – 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} }
count (integer) – number of executions of Brainvisa
expiredRuns (dictonary) – 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.
- brainvisa.configuration.neuroConfig.chooseDatabaseVersionSyncOption(context)[source]¶
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.
- Parameters
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.
- brainvisa.configuration.neuroConfig.environmentHTML()[source]¶
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.
- brainvisa.configuration.neuroConfig.findInPath(file, pathlist=['/casa/host/build/build_files/axon/../../bin', '/casa/host/src/development/casa-distro/5.1/cbin', '/casa/host/build/bin', '/casa/host/build/bin', '/casa/casa-distro/cbin', '/usr/local/sbin', '/usr/local/bin', '/usr/sbin', '/usr/bin', '/sbin', '/bin', '/casa/host/bootstrap/brainvisa-cmake/bin', '/casa/bootstrap/brainvisa-cmake/bin'], is_dir=False)[source]¶
Returns the directory containing file
- brainvisa.configuration.neuroConfig.findPlatform()[source]¶
Identify system platform, possible return values are :
‘windows’: Windows
‘linux’: Linux
‘sunos’: SunOS (Solaris)
‘darwin’: Darwin (MacOS X)
‘irix’: Irix
None: unknown
- brainvisa.configuration.neuroConfig.getDocFile(filename)[source]¶
Search doc file in doc path and if not found, in english documentation path.
- brainvisa.configuration.neuroConfig.getDocPath(path, project='')[source]¶
Returns the path of the documentation directory of the given project.
Returns BrainVISA share directory path.
- brainvisa.configuration.neuroConfig.initializeOntologyPaths()[source]¶
Initializes the global variables
typesPath
andfileSystemOntologiesPath
. This function is used when toolboxes are reloaded.
- brainvisa.configuration.neuroConfig.openDebugFile(fileName)[source]¶
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.
- brainvisa.configuration.neuroConfig.stdinLoop()[source]¶
Reads Brainvisa commands on stdin and executes them.
brainvisa.configuration.axon_capsul_config_link¶
brainvisa.configuration.brainvisa_configuration¶
@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>}
- class brainvisa.configuration.brainvisa_configuration.BrainVISAConfiguration[source]¶
Bases:
soma.configuration.ConfigurationGroup
- brainvisa.configuration.brainvisa_configuration.defaultCSVViewer()[source]¶
If a real CSV viewer is found, use it dy default. If there is no CSV viewer available, the built-in Qt viewer is used.
brainvisa.configuration.anatomist_configuration¶
@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>}
brainvisa.configuration.databases_configuration¶
@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>}
- class brainvisa.configuration.databases_configuration.DatabaseSettings(directory=None, selected=True, read_only=False)[source]¶
Bases:
soma.signature.signature.HasSignature
- class brainvisa.configuration.databases_configuration.DatabasesConfiguration(*args, **kwargs)[source]¶
Bases:
soma.configuration.ConfigurationGroup
- class brainvisa.configuration.databases_configuration.ExpertDatabaseSettings[source]¶
Bases:
soma.signature.signature.HasSignature
- class brainvisa.configuration.databases_configuration.FormatsSequence[source]¶
Bases:
soma.signature.attributetypes.sequence.Sequence
A L{Sequence} is a L{DataType} for Python sequence whose elements are all of the same type.
@type elementType: any value accepted by L{DataType.dataTypeInstance} @param elementType: type of all elements in the sequence @type minSize: positive integer @param minSize: minimum number of elements in the sequence (default = 0) @type maxSize: None or positive integer @param maxSize: maximum number of elements in the sequence. If value is C{None} (the default), there is no limit on the sequence size.
brainvisa.configuration.fsl_configuration¶
@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>}
brainvisa.configuration.matlab_configuration¶
@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>}
brainvisa.configuration.mpegConfig¶
brainvisa.configuration.spm_configuration¶
@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>}
brainvisa.configuration.r_configuration¶
@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>}
brainvisa.configuration.soma_workflow_configuration¶
brainvisa.configuration.qt4gui¶
- class brainvisa.configuration.qt4gui.neuroConfigGUI.BugReportDialog(parent=None, name=None)[source]¶
Bases:
PyQt5.QtWidgets.QWidget
- brainvisa.configuration.qt4gui.neuroConfigGUI.editConfiguration()[source]¶
Opens Brainvisa options window. When the user closes the window, the configuration is saved in Brainvisa options file.
Some options are taken into account immediately:
if databases selection has changed, databases are reloaded
if userLevel has changed, the list of available processes is updated
new HTML browser and new text editors are taken into account
language change is applied to documentation pages.
Some other options are not applied directly but are saved in the options file and will be applied next time Brainvisa is started.
@author: Dominique Geffroy @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>}
- class brainvisa.configuration.qt4gui.databases_configuration_qt4gui.DatabaseManagerGUI(parent=None, name=None)[source]¶
Bases:
PyQt5.QtWidgets.QWidget
- class brainvisa.configuration.qt4gui.databases_configuration_qt4gui.DatabasesConfiguration_Qt4GUI(dataType)[source]¶
Bases:
soma.qt4gui.automatic.Qt4GUI
Constructors of L{Qt4GUI} (and its derived classes) must accept a single C{dataType} parameter representing the type of data that can be view or edited by this GUI element. @param dataType: type data that this L{Qt4GUI} can handle. This can be any value accepted by L{DataType.dataTypeInstance}.
- closeEditionWidget(editionWidget)[source]¶
Close a widget (and free associated ressources) created by C{self.L{editionWidget}}.
- editionWidget(object, parent=None, name=None, live=False)[source]¶
Create a widget for editing an object.
- class brainvisa.configuration.qt4gui.databases_configuration_qt4gui.FormatsSequence_Qt4GUI(dataType)[source]¶
Bases:
soma.qt4gui.automatic.Qt4GUI
Constructors of L{Qt4GUI} (and its derived classes) must accept a single C{dataType} parameter representing the type of data that can be view or edited by this GUI element. @param dataType: type data that this L{Qt4GUI} can handle. This can be any value accepted by L{DataType.dataTypeInstance}.
- closeEditionWidget(editionWidget)[source]¶
Close a widget (and free associated ressources) created by C{self.L{editionWidget}}.
- editionWidget(object, parent=None, name=None, live=False)[source]¶
Create a widget for editing an object.
@author: Dominique Geffroy @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>}
- class brainvisa.configuration.qt4gui.matlab_configuration_qt4gui.MatlabConfiguration_Qt4GUI(instance)[source]¶
Bases:
soma.qt4gui.automatic.Qt4GUI
This class adds a ‘guess configuration’ button to default GUI.
Constructors of L{Qt4GUI} (and its derived classes) must accept a single C{dataType} parameter representing the type of data that can be view or edited by this GUI element. @param dataType: type data that this L{Qt4GUI} can handle. This can be any value accepted by L{DataType.dataTypeInstance}.
- closeEditionWidget(editionWidget)[source]¶
Close a widget (and free associated ressources) created by C{self.L{editionWidget}}.
- editionWidget(value, parent=None, name=None, live=False)[source]¶
Create a widget for editing an object.
- class brainvisa.configuration.qt4gui.spm_configuration_qt4gui.SPMConfiguration_Qt4GUI(instance)[source]¶
Bases:
soma.qt4gui.automatic.Qt4GUI
This class adds a ‘guess configuration’ button to default GUI.
Constructors of L{Qt4GUI} (and its derived classes) must accept a single C{dataType} parameter representing the type of data that can be view or edited by this GUI element. @param dataType: type data that this L{Qt4GUI} can handle. This can be any value accepted by L{DataType.dataTypeInstance}.
- closeEditionWidget(editionWidget)[source]¶
Close a widget (and free associated ressources) created by C{self.L{editionWidget}}.
- editionWidget(value, parent=None, name=None, live=True)[source]¶
Create a widget for editing an object.