# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. 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.
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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/>.
#
#
# CITATION:
# When using The Virtual Brain for scientific publications, please cite it as explained here:
# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications
#
#
"""
The Pattern datatypes.
.. moduleauthor:: Stuart A. Knock <Stuart@tvb.invalid>
"""
import numpy
from tvb.datatypes import surfaces, volumes, connectivity, equations
from tvb.basic.neotraits.api import HasTraits, NArray, Attr
[docs]
class SpatialPattern(HasTraits):
"""
Equation for space variation.
"""
spatial = Attr(field_type=equations.FiniteSupportEquation, label="Spatial Equation")
space = None
_spatial_pattern = None
[docs]
def summary_info(self):
"""
Gather scientifically interesting summary information from an instance of this DataType.
"""
return {"Type": self.__class__.__name__,
"Spatial equation": self.spatial.__class__.__name__,
"Spatial parameters": self.spatial.parameters}
@property
def spatial_pattern(self):
"""
Return a discrete representation of the spatial pattern.
"""
return self._spatial_pattern
[docs]
class SpatioTemporalPattern(SpatialPattern):
"""
Combine space and time equations.
"""
temporal = Attr(field_type=equations.TemporalApplicableEquation, label="Temporal Equation")
# space must be shape (x, 1); time must be shape (1, t)
time = None
_temporal_pattern = None
[docs]
def summary_info(self):
""" Extend the base class's summary dictionary. """
summary = super(SpatioTemporalPattern, self).summary_info()
summary["Temporal equation"] = self.temporal.__class__.__name__
summary["Temporal parameters"] = self.temporal.parameters
return summary
@property
def temporal_pattern(self):
"""
Return a discrete representation of the temporal pattern.
"""
return self._temporal_pattern
def __call__(self, temporal_indices=None, spatial_indices=None):
"""
The temporal pattern vector, set by the configure_time method, is
combined with the spatial pattern vector, set by the configure_space
method, to form a spatiotemporal pattern.
Called with a single time index as an argument, the spatial pattern at
that point in time is returned. This is the standard usage within a
simulation where the current simulation time point is retrieved.
Called without any arguments, by default a big array representing the
entire spatio-temporal pattern is returned. While this may be useful for
visualisation, say of region level spatio-temporal patterns, care should
be taken as when surfaces are considered the returned array can be
potentially quite large.
"""
pattern = None
if temporal_indices is not None and spatial_indices is None:
pattern = self._spatial_pattern * self._temporal_pattern[0, temporal_indices]
elif temporal_indices is None and spatial_indices is None:
pattern = self._spatial_pattern * self._temporal_pattern
elif temporal_indices is not None and spatial_indices is not None:
pattern = self._spatial_pattern[spatial_indices, 0] * self._temporal_pattern[0, temporal_indices]
elif temporal_indices is None and spatial_indices is not None:
pattern = self._spatial_pattern[spatial_indices, 0] * self._temporal_pattern
else:
self.log.error("%s: Well, that shouldn't be possible..." % repr(self))
return pattern
[docs]
class StimuliRegion(SpatioTemporalPattern):
"""
A class that bundles the temporal profile of the stimulus, together with the
list of scaling weights of the regions where it will applied.
"""
connectivity = Attr(field_type=connectivity.Connectivity, label="Connectivity")
spatial = Attr(field_type=equations.DiscreteEquation,
label="Spatial Equation",
default=equations.DiscreteEquation()) # fixed_type=True, order=-1)
weight = NArray(label="scaling") # , locked=True, order=4)
[docs]
@staticmethod
def get_default_weights(number_of_regions):
"""
Returns a list with a number of elements
equal to the given number of regions.
"""
return numpy.array([0.0] * number_of_regions)
@property
def weight_array(self):
"""
Wrap weight List into a Numpy array, as it is requested by the simulator.
"""
return numpy.array(self.weight)[:, numpy.newaxis]
[docs]
class StimuliSurface(SpatioTemporalPattern):
"""
A spatio-temporal pattern defined in a Surface DataType.
It includes the list of focal points.
"""
surface = Attr(field_type=surfaces.CorticalSurface, label="Surface")
focal_points_triangles = NArray(dtype=int, label="Focal points triangles") # , locked=True, order=4)
@property
def focal_points_surface(self):
focal_points = []
if self.surface is None or self.surface.triangles is None:
self.log.warning('Focal points list will be empty. Load the surface triangles before accessing this property!')
return numpy.array(focal_points)
for triangle_index in self.focal_points_triangles:
focal_points.append(int(self.surface.triangles[triangle_index][0]))
return numpy.array(focal_points)
[docs]
class SpatialPatternVolume(SpatialPattern):
""" A spatio-temporal pattern defined in a volume. """
volume = Attr(volumes.Volume, label="Volume")
focal_points_volume = NArray(dtype=int, label="Focal points")
