Source code for tvb.core.neotraits.db
# -*- 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 http://www.thevirtualbrain.org
#
# (c) 2012-2023, 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 <http://www.gnu.org/licenses/>.
#
#
# CITATION:
# When using The Virtual Brain for scientific publications, please cite it as explained here:
# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications
#
#
import uuid
import numpy
from datetime import datetime
from sqlalchemy import Column, Integer, Text, DateTime, String, Boolean
from sqlalchemy.orm import declarative_base, declared_attr
SCALAR_MAPPING = {
bool: Boolean,
int: Integer,
str: String
}
Base = declarative_base(name='DeclarativeBase')
[docs]class HasTraitsIndex(Base):
id = Column(Integer, primary_key=True)
gid = Column(String(32), unique=True)
type_ = Column(String(50))
title = Column(Text)
create_date = Column(DateTime, default=datetime.now)
# Quick remainder about @declared_attr. It makes a class method.
# Sqlalchemy will treat this class method like a statically declared class attribute
# Another quick remainder, class methods are polymorphic
@declared_attr
def __tablename__(cls):
# subclasses no longer need to define the __tablename__ as we do it here polymorphically for them.
return cls.__name__
@declared_attr
def __mapper_args__(cls):
"""
A polymorphic __maper_args__. Because of it the subclasses no longer need to declare the polymorphic_identity
"""
# this gets called by sqlalchemy before the HasTraitsIndex class declaration is finished (in it's metatype)
# so we have to refer to the type by name
if cls.__name__ == 'HasTraitsIndex' and cls.__module__ == __name__:
# for the base class we have to define the discriminator column
return {
'polymorphic_on': cls.type_,
'polymorphic_identity': cls.__name__
}
elif cls.__name__ == "DataType":
return {
'polymorphic_identity': cls.__name__,
'inherit_condition': cls.id == HasTraitsIndex.id
}
else:
return {
'polymorphic_identity': cls.__name__
}
def __init__(self):
super(HasTraitsIndex, self).__init__()
self.type_ = type(self).__name__
self.gid = uuid.uuid4().hex
def __repr__(self):
cls = type(self)
return '<{}.{} gid="{}..." id="{}">'.format(
cls.__module__, cls.__name__, self.gid[:4], self.id
)
[docs] def get_subtype_attr(self):
return None
[docs]def ensure_float(data):
return numpy.float64(data)
[docs]def ensure_int(data):
return int(data)
[docs]def from_ndarray(array):
if array is None:
return None
if array.dtype.kind in 'iufc' and array.size != 0:
# we compute these simple statistics for integer unsigned float or complex
# arrays that are not empty
min_value, max_value, mean_value = ensure_float(array.min()), ensure_float(array.max()),\
ensure_float(array.mean())
else:
min_value, max_value, mean_value = None, None, None
return min_value, max_value, mean_value
