Source code for tvb.adapters.datatypes.h5.annotation_h5

# -*- 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 to download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also
# (c) 2012-2024, 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 explained here:

.. moduleauthor:: Lia Domide <>

import numpy
from tvb.basic.neotraits.api import NArray, Attr, HasTraits
from tvb.core.neotraits.h5 import H5File, DataSet, Reference, STORE_STRING
from tvb.datatypes.connectivity import Connectivity

ANNOTATION_DTYPE = numpy.dtype([('id', 'i'),
                                ('parent_id', 'i'),
                                ('parent_left', 'i'),
                                ('parent_right', 'i'),
                                ('relation', STORE_STRING),  # S16
                                ('label', STORE_STRING),  # S256
                                ('definition', STORE_STRING),  # S1024
                                ('synonym', STORE_STRING),  # S2048
                                ('uri', STORE_STRING),  # S256
                                ('synonym_tvb_left', 'i'),
                                ('synonym_tvb_right', 'i')

[docs] class ConnectivityAnnotations(HasTraits): """ Ontology annotations for a Connectivity. """ connectivity = Attr(field_type=Connectivity) """ Holds a flatten form for the annotations for a full connectivity. Each region in the connectivity can have None, or a tree of AnnotationTerms To be stored in a compound DS in H5. """ region_annotations = NArray( default=numpy.array([], dtype=ANNOTATION_DTYPE), dtype=ANNOTATION_DTYPE, label="Region Annotations", doc="""Flat tree of annotations for every connectivity region.""")
[docs] def set_annotations(self, annotation_terms): annotations = [ann.to_tuple() for ann in annotation_terms] annotations = numpy.array(annotations, dtype=ANNOTATION_DTYPE) self.region_annotations = annotations
[docs] def get_activation_patterns(self): """ Group Annotation terms by URI. :return: map {brco_id: list of TVB regions IDs in which the same term is being subclass} """ map_by_uri = {} for ann in self.region_annotations: ann_uri = ann[8] left, right = str(ann[2]), str(ann[3]) if ann_uri not in map_by_uri: map_by_uri[ann_uri] = [left, right] else: if left not in map_by_uri[ann_uri]: map_by_uri[ann_uri].append(left) if right not in map_by_uri[ann_uri]: map_by_uri[ann_uri].append(right) map_by_brco_id = {} for ann in self.region_annotations: ann_uri = ann[8] ann_id = ann[0] map_by_brco_id[str(ann_id)] = map_by_uri[ann_uri] return map_by_brco_id
[docs] class ConnectivityAnnotationsH5(H5File): """ Ontology annotations for a Connectivity. """ def __init__(self, path): super(ConnectivityAnnotationsH5, self).__init__(path) self.region_annotations = DataSet(ConnectivityAnnotations.region_annotations, self) self.connectivity = Reference(ConnectivityAnnotations.connectivity, self)
[docs] def store(self, datatype, scalars_only=False, store_references=True): # type: (ConnectivityAnnotations, bool, bool) -> None super(ConnectivityAnnotationsH5, self).store(datatype, scalars_only, store_references)