The Virtual Brain Project

Source code for tvb.adapters.uploaders.brco_importer

# -*- coding: utf-8 -*-
# TheVirtualBrain-Framework Package. This package holds all Data Management, and 
# Web-UI helpful to run brain-simulations. To use it, you also need do download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also
# (c) 2012-2017, Baycrest Centre for Geriatric Care ("Baycrest") and others
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.  See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program.  If not, see <>.
# When using The Virtual Brain for scientific publications, please cite it as follows:
#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

.. moduleauthor:: Lia Domide <>

from tvb.adapters.uploaders.abcuploader import ABCUploader
from tvb.adapters.uploaders.brco.parser import XMLParser
from tvb.core.adapters.exceptions import LaunchException
from import transactional
from tvb.datatypes.connectivity import Connectivity
from tvb.datatypes.annotations import ConnectivityAnnotations

[docs]class BRCOImporter(ABCUploader): """ Import connectivity data stored in the networkx gpickle format """ _ui_name = "BRCO Ontology Annotations" _ui_subsection = "brco_importer" _ui_description = "Import connectivity annotations from BRCO Ontology"
[docs] def get_upload_input_tree(self): """ Take as input a mat file """ return [{'name': 'data_file', 'type': 'upload', 'required_type': '.xml', 'label': 'Connectivity Annotations', 'required': True}, {'name': 'connectivity', 'label': 'Target Large Scale Connectivity', 'type': Connectivity, 'required': True, 'datatype': True, 'description': 'The Connectivity for which these annotations were made'}, ]
[docs] def get_output(self): return [ConnectivityAnnotations]
[docs] def launch(self, data_file, connectivity): try: result = ConnectivityAnnotations(connectivity=connectivity, storage_path=self.storage_path) parser = XMLParser(data_file, connectivity) annotations = parser.read_annotation_terms() result.set_annotations(annotations) return result except Exception as excep: self.log.exception("Could not process Connectivity Annotations") raise LaunchException(excep)