The Virtual Brain Project

Source code for tvb.adapters.uploaders.networkx_importer

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"""
.. moduleauthor:: Mihai Andrei <mihai.andrei@codemart.ro>
"""

import networkx
from tvb.adapters.uploaders.abcuploader import ABCUploader
from tvb.adapters.uploaders.networkx_connectivity.parser import NetworkxParser
from tvb.core.adapters.exceptions import ParseException, LaunchException
from tvb.core.entities.storage import transactional
from tvb.datatypes.connectivity import Connectivity


[docs]class NetworkxConnectivityImporter(ABCUploader): """ Import connectivity data stored in the networkx gpickle format """ _ui_name = "Connectivity Networkx gpickle" _ui_subsection = "networkx_importer" _ui_description = "Import connectivity data stored in the networkx gpickle format"
[docs] def get_upload_input_tree(self): tree = [{'name': 'data_file', 'type': 'upload', 'required_type': '.gpickle', 'label': 'Please select file to import', 'required': True}] tree.extend(NetworkxParser.prepare_input_params_tree()) return tree
[docs] def get_output(self): return [Connectivity]
@transactional
[docs] def launch(self, data_file, **kwargs): try: parser = NetworkxParser(self.storage_path, **kwargs) net = networkx.read_gpickle(data_file) connectivity = parser.parse(net) return [connectivity] except ParseException as excep: self.log.exception("Could not process Connectivity") raise LaunchException(excep)