Axon python API modules ======================= This part of the API is in the Python path, it may be imported without running Brainvisa. Modules organization -------------------- - :py:mod:`brainvisa.axon`: loading Brainvisa in a Python script. - :py:mod:`brainvisa.processes`: classes about processes and pipelines. - :py:mod:`brainvisa.anatomist`: specialization of pyanatomist API for Brainvisa. Used by most of Brainvisa viewers. - :py:mod:`brainvisa.toolboxes`: Toolbox class representing a BrainVISA toolbox. - :py:mod:`brainvisa.shelltools`: functions to copy, move, delete files. - :py:mod:`brainvisa.workflow`: Conversion of a Process into a Workflow usable in :somaworkflow:`Soma-workflow `. - :py:mod:`brainvisa.validation`: Definition of an exception that can be raised by processes validation functions. - :py:mod:`brainvisa.history`: Framework to manage history of processes. - :py:mod:`brainvisa.multipleExecfile`: A class to load several inter-dependent python files. - :py:mod:`brainvisa.registration`: referentials and transformations management. brainvisa.configuration +++++++++++++++++++++++ This module contains the classes that manage BrainVisa set of options, accessible throught the menu BrainVISA -> Preferences. - :py:mod:`brainvisa.configuration.api`: Initialization of the configuration object that contains the user preferences. - :py:mod:`brainvisa.configuration.neuroConfig`: global variables describing configuration parameters and user preferences. - :py:mod:`brainvisa.configuration.anatomist_configuration`: options about Anatomist. - :py:mod:`brainvisa.configuration.brainvisa_configuration`: general options. - :py:mod:`brainvisa.configuration.databases_configuration`: options about the databases. - :py:mod:`brainvisa.configuration.fsl_configuration`: options about FSL. - :py:mod:`brainvisa.configuration.matlab_configuration`: options about Matlab. - :py:mod:`brainvisa.configuration.spm_configuration`: options about SPM. - :py:mod:`brainvisa.configuration.r_configuration`: options about R. - :py:mod:`brainvisa.configuration.qt4gui`: specific graphical user interface for options about databases and Matlab. - :py:mod:`brainvisa.configuration.mpegConfig` - :py:mod:`brainvisa.configuration.soma_workflow_configuration`: :somaworkflow:`Soma-Workflow-related config ` - :py:mod:`brainvisa.configuration.qt4gui.neuroConfigGUI`: Bug report dialog. .. _brainvisa.data: brainvisa.data ++++++++++++++ - :py:mod:`brainvisa.data.neuroData`: classes defining the signature of a process, parameter types. - :py:mod:`brainvisa.data.neuroDiskItems`: class DiskItem that defines data and matching files. - :py:mod:`brainvisa.data.neuroHierarchy`: databases creation and initialization. - :py:mod:`brainvisa.data.fileSystemOntology`: classes to define a BrainVISA ontology. - :py:mod:`brainvisa.data.sqlFSODatabase` - :py:mod:`brainvisa.data.readdiskitem` - :py:mod:`brainvisa.data.writediskitem` - :py:mod:`brainvisa.data.actions` - :py:mod:`brainvisa.data.databaseCheck` - :py:mod:`brainvisa.data.directory_iterator` - :py:mod:`brainvisa.data.fileformats` - :py:mod:`brainvisa.data.ftpDirectory` - :py:mod:`brainvisa.data.labelSelection` - :py:mod:`brainvisa.data.minfExtensions`: declaration of the type of objects that can be written in minf format. - :py:mod:`brainvisa.data.patterns` - :py:mod:`brainvisa.data.sql` - :py:mod:`brainvisa.data.temporary` - :py:mod:`brainvisa.data.virtualDirectory` - :py:mod:`brainvisa.data.qt4gui` brainvisa.processing ++++++++++++++++++++ - :py:mod:`brainvisa.processing.axon_fso_to_fom`: convert Axon File System Organization (hierarchies) to :capsul:`CAPSUL File Orgnaization Models `. - :py:mod:`brainvisa.processing.axon_to_capsul`: convert Axon processes and pipelines :capsul:`CAPSUL processes or pipelines `. - :py:mod:`brainvisa.processing.capsul_process`: wrapper class to make a :capsul:`CAPSUL process or pipeline ` available as an Axon process. - :py:mod:`brainvisa.processing.neuroException`: classes and functions defining error and warning messages. - :py:mod:`brainvisa.processing.neuroLog`: creation of BrainVISA log file. - :py:mod:`brainvisa.processing.process_based_viewer`: specialized viewer process, which works with a process or pipeline to get its parameters brainvisa.tools +++++++++++++++ - :py:mod:`brainvisa.tools.aimsGlobals`: definition of named lists of formats. - :py:mod:`brainvisa.tools.mainthreadlife`: ensure an object is deleted in the main thread. - :py:mod:`brainvisa.tools.matlabValidation`: validation function that checks if matlab is enabled. - :py:mod:`brainvisa.tools.spm_conversion` - :py:mod:`brainvisa.tools.spm_registration` - :py:mod:`brainvisa.tools.spm_results` - :py:mod:`brainvisa.tools.spm_run` - :py:mod:`brainvisa.tools.spm_segmentation` - :py:mod:`brainvisa.tools.spm_utils` - :py:mod:`brainvisa.tools.DisplayResultsFromSPM` - :py:mod:`brainvisa.tools.displayTitledGrid` .. _brainvisa.processing.qt4gui: brainvisa.processing.qt4gui: GUI Modules +++++++++++++++++++++++++++++++++++++++++ The classes related to the graphical user interface are located in ``qt4gui`` modules. They use `PyQt API `_, a set of Python bindings for `Qt application framework `_: - :py:mod:`brainvisa.processing.qtgui.backwardCompatibleQt`: it has been used to keep backward compatibility with old versions of PyQt. - :py:mod:`brainvisa.processing.qt4gui.neuroProcessesGUI`: BrainVISA main window and processes windows. - :py:mod:`brainvisa.processing.qt4gui.neuroExceptionGUI`: Error and warning messages window. - :py:mod:`brainvisa.processing.qt4gui.neuroLogGUI`: Log window. - :py:mod:`brainvisa.processing.qt4gui.command`: class CommandWithQProcess used to call commands in Brainvisa processes. This module is not related to the graphical user interface but it uses Qt, that's why it is in ``qt4gui`` module. Some ``qtgui`` modules also exist but are mainly just redirections to the corresponding ``qt4gui`` module. It was useful when we maintained the compatibility with qt3 but is no more the case. Note that the ``qt4gui`` modules do work for both Qt4 and Qt5. brainvisa.data.qt4gui: GUI Modules ++++++++++++++++++++++++++++++++++ - :py:mod:`brainvisa.data.qt4gui.databaseCheckGUI` - :py:mod:`brainvisa.data.qt4gui.diskItemBrowser` - :py:mod:`brainvisa.data.qt4gui.hierarchyBrowser` - :py:mod:`brainvisa.data.qt4gui.history` - :py:mod:`brainvisa.data.qt4gui.labelSelectionGUI` - :py:mod:`brainvisa.data.qt4gui.neuroDataGUI`: Editor windows for the parameter types defined in :py:mod:`brainvisa.data.neuroData`. - :py:mod:`brainvisa.data.qt4gui.readdiskitemGUI` - :py:mod:`brainvisa.data.qt4gui.scalarFeaturesViewer` - :py:mod:`brainvisa.data.qt4gui.updateDatabases` brainvisa.shelltools -------------------- .. automodule:: brainvisa.shelltools :members: :show-inheritance: brainvisa.anatomist: a specialized wrapper for Anatomist -------------------------------------------------------- .. automodule:: brainvisa.anatomist :members: :show-inheritance: brainvisa.toolboxes ------------------- .. automodule:: brainvisa.toolboxes :members: :show-inheritance: brainvisa.workflow ------------------ .. automodule:: brainvisa.workflow :members: :show-inheritance: brainvisa.validation -------------------- .. automodule:: brainvisa.validation :members: :show-inheritance: brainvisa.history ----------------- .. automodule:: brainvisa.history :members: :show-inheritance: brainvisa.multipleExecfile -------------------------- .. automodule:: brainvisa.multipleExecfile :members: :show-inheritance: brainvisa.registration ---------------------- .. automodule:: brainvisa.registration :members: :show-inheritance: