# -*- 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 tvb.basic.neotraits.api import HasTraits, Attr
from tvb.basic.neotraits.ex import TraitAttributeError
from tvb.core.entities.generic_attributes import GenericAttributes
[docs]class ViewModel(HasTraits):
operation_group_gid = Attr(field_type=uuid.UUID, required=False)
ranges = Attr(str, required=False)
range_values = Attr(str, required=False)
is_metric_operation = Attr(bool, default=False)
def __init__(self, **kwargs):
super(ViewModel, self).__init__(**kwargs)
self.create_date = datetime.now()
self.generic_attributes = GenericAttributes()
[docs] def linked_has_traits(self):
return HasTraits
[docs]class Str(Attr):
def __init__(self, field_type=str, default=None, doc='', label='', required=True,
final=False, choices=None):
super(Str, self).__init__(field_type, default, doc, label, required, final, choices)
[docs]class DataTypeGidAttr(Attr):
"""
Keep a GID but also link the type of DataType it should point to
"""
def __init__(self, linked_datatype, field_type=uuid.UUID, filters=None, default=None, doc='', label='',
required=True, final=False, choices=None):
super(DataTypeGidAttr, self).__init__(field_type, default, doc, label, required, final, choices)
self.linked_datatype = linked_datatype
self.filters = filters
def __set__(self, instance, value):
if isinstance(value, str):
try:
value = uuid.UUID(value)
except ValueError:
raise TraitAttributeError("Given value cannot be used as UUID for field {}".format(self.field_name))
super(DataTypeGidAttr, self).__set__(instance, value)
[docs]class EquationAttr(Attr):
"""
# TODO: there are places where we need eq params as a nested form. Figure out a proper model
"""
[docs]def replace_nan_values(input_data):
""" Replace NAN values with a given values"""
is_any_value_nan = False
if not numpy.isfinite(input_data).all():
for idx in range(len(input_data)):
input_data[idx] = numpy.nan_to_num(input_data[idx])
is_any_value_nan = True
return is_any_value_nan
