The Virtual Brain Project

Source code for tvb.adapters.uploaders.gifti_surface_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 http://www.thevirtualbrain.org
#
# (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.
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# 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 <http://www.gnu.org/licenses/>.
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#
#   CITATION:
# 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:: Mihai Andrei <mihai.andrei@codemart.ro>
.. moduleauthor:: Calin Pavel <calin.pavel@codemart.ro>
"""

from tvb.adapters.uploaders.abcuploader import ABCUploader
from tvb.adapters.uploaders.gifti.parser import GIFTIParser, OPTION_READ_METADATA
from tvb.basic.logger.builder import get_logger
from tvb.core.adapters.exceptions import LaunchException, ParseException
from tvb.core.entities.storage import dao
from tvb.datatypes.surfaces import Surface, ALL_SURFACES_SELECTION



[docs]class GIFTISurfaceImporter(ABCUploader): """ This importer is responsible for import of surface from GIFTI format (XML file) and store them in TVB as Surface. """ _ui_name = "Surface GIFTI" _ui_subsection = "gifti_surface_importer" _ui_description = "Import a surface from GIFTI"
[docs] def get_upload_input_tree(self): """ Take as input a .GII file. """ surface_options = [{'name': 'Specified in the file metadata', 'value': OPTION_READ_METADATA}] surface_options.extend(ALL_SURFACES_SELECTION) return [{'name': 'file_type', 'type': 'select', 'label': 'Specify file type : ', 'required': True, 'options': surface_options, 'default': OPTION_READ_METADATA}, {'name': 'data_file', 'type': 'upload', 'required_type': '.gii', 'required': True, 'label': 'Please select a .gii (LH if cortex)'}, {'name': 'data_file_part2', 'type': 'upload', 'required_type': '.gii', 'required': False, 'label': "Optionally select 2'nd .gii (RH if cortex)"}, {'name': 'should_center', 'type': 'bool', 'default': False, 'label': 'Center surface using vertex means along axes'} ]
[docs] def get_output(self): return [Surface]
[docs] def launch(self, file_type, data_file, data_file_part2, should_center=False): """ Execute import operations: """ parser = GIFTIParser(self.storage_path, self.operation_id) try: surface = parser.parse(data_file, data_file_part2, file_type, should_center=should_center) validation_result = surface.validate() if validation_result.warnings: self.add_operation_additional_info(validation_result.summary()) return [surface] except ParseException as excep: logger = get_logger(__name__) logger.exception(excep) raise LaunchException(excep)