The Virtual Brain Project

Source code for tvb.interfaces.command.demos.datatypes.read_from_h5

# -*- coding: utf-8 -*-
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# 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
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#   CITATION:
# When using The Virtual Brain for scientific publications, please cite it as follows:
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#   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)
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"""
Demo script on how to read a TVB H5 file

.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
"""

if __name__ == "__main__":
    from tvb.basic.profile import TvbProfile
    TvbProfile.set_profile(TvbProfile.COMMAND_PROFILE)

import os
import sys
from tvb.core.entities import model
from tvb.core.entities.storage import dao
from tvb.core.services.import_service import ImportService


[docs]def read_h5(full_paths): # We need to load the DataType in the context of an operation, and a project all_projects = dao.get_all_projects() all_operations = dao.get_generic_entity(model.Operation, all_projects[0].id, "fk_launched_in") service = ImportService() results = [] for full_path in full_paths: # The actual read of H5: datatype = service.load_datatype_from_file(full_path, all_operations[0].id) print("We've build DataType: [%s]" % datatype.__class__.__name__, datatype) results.append(datatype) return results
if __name__ == '__main__': if len(sys.argv) > 1: FILE_PATHS = sys.argv[1:] else: import tvb_data.h5 dir_name = os.path.dirname(tvb_data.h5.__file__) FILE_PATHS = [os.path.join(dir_name, "Connectivity_74.h5"), os.path.join(dir_name, "TimeSeriesRegion.h5")] print("We will try to read from H5: " + str(FILE_PATHS)) read_h5(FILE_PATHS)