class StimuliRegionData(SpatioTemporalPatternData):
"""
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 = connectivity_module.Connectivity(label="Connectivity",
order=1)
spatial = equations.DiscreteEquation(label="Spatial Equation",
default=equations.DiscreteEquation,
fixed_type=True,
order=-1)
weight = basic.List(label="scaling", locked=True, order=4)
def test_stimuliregion(self):
conn = connectivity.Connectivity(load_default=True)
conn.configure()
dt = patterns.StimuliRegion()
dt.connectivity = conn
dt.spatial = equations.DiscreteEquation()
dt.temporal = equations.Gaussian()
dt.weight = [0 for _ in range(conn.number_of_regions)]
dt.configure_space()
assert dt.summary_info['Type'] == 'StimuliRegion'
assert dt.connectivity is not None
assert dt.space.shape == (76, 1)
assert dt.spatial_pattern.shape == (76, 1)
assert isinstance(dt.temporal, equations.Gaussian)
assert dt.temporal_pattern is None
assert dt.time is None
def test_stimuliregion(self):
conn = connectivity.Connectivity()
conn.configure()
dt = patterns.StimuliRegion()
dt.connectivity = conn
dt.spatial = equations.DiscreteEquation()
dt.temporal = equations.Gaussian()
dt.weight = [0 for _ in range(conn.number_of_regions)]
dt.configure_space()
self.assertEqual(dt.summary_info['Type'], 'StimuliRegion')
self.assertTrue(dt.connectivity is not None)
self.assertEqual(dt.space.shape, (74, 1))
self.assertEqual(dt.spatial_pattern.shape, (74, 1))
self.assertTrue(isinstance(dt.temporal, equations.Gaussian))
self.assertTrue(dt.temporal_pattern is None)
self.assertTrue(dt.time is None)
def test_stimulisurface(self):
srf = surfaces.CorticalSurface.from_file()
srf.configure()
dt = patterns.StimuliSurface()
dt.surface = srf
dt.spatial = equations.DiscreteEquation()
dt.temporal = equations.Gaussian()
dt.focal_points_triangles = numpy.array([0, 1, 2])
dt.configure()
dt.configure_space()
summary = dt.summary_info()
assert summary['Type'] == "StimuliSurface"
assert dt.space.shape == (16384, 3)
assert isinstance(dt.spatial, equations.DiscreteEquation)
assert dt.spatial_pattern.shape == (16384, 1)
assert dt.surface is not None
assert isinstance(dt.temporal, equations.Gaussian)
assert dt.temporal_pattern is None
assert dt.time is None
def __init__(self,
connectivity=None,
spatial=None,
weight=None,
*args,
**kwargs):
if connectivity is None:
connectivity = conn.Connectivity()
self.connectivity = connectivity
# lives in base class
if spatial is None:
spatial = equations.DiscreteEquation()
if weight is None:
weight = []
self.weight = weight
super(StimuliRegion, self).__init__(*args, spatial=spatial, **kwargs)
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 = connectivity.Connectivity(label="Connectivity", order=1)
spatial = equations.DiscreteEquation(label="Spatial Equation",
default=equations.DiscreteEquation,
fixed_type=True,
order=-1)
weight = basic.List(label="scaling", locked=True, order=4)
@staticmethod
def get_default_weights(number_of_regions):
"""
Returns a list with a number of elements
equal to the given number of regions.
"""
return [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]
def configure_space(self, region_mapping=None):
"""
Do necessary preparations in order to use this stimulus.
NOTE: this was previously done in simulator configure_stimuli() method.
It no needs to be used in stimulus viewer also.
"""
if region_mapping is not None:
#TODO: smooth at surface region boundaries
distance = self.weight_array[region_mapping, :]
else:
distance = self.weight_array
super(StimuliRegion, self).configure_space(distance)
def test_stimulisurface(self):
srf = surfaces.CorticalSurface(load_default=True)
srf.configure()
dt = patterns.StimuliSurface()
dt.surface = srf
dt.spatial = equations.DiscreteEquation()
dt.temporal = equations.Gaussian()
dt.focal_points_surface = [0, 1, 2]
dt.focal_points_triangles = [0, 1, 2]
dt.configure()
dt.configure_space()
summary = dt.summary_info
self.assertEqual(summary['Type'], "StimuliSurface")
self.assertEqual(dt.space.shape, (16384, 3))
self.assertTrue(isinstance(dt.spatial, equations.DiscreteEquation))
self.assertEqual(dt.spatial_pattern.shape, (16384, 1))
self.assertTrue(dt.surface is not None)
self.assertTrue(isinstance(dt.temporal, equations.Gaussian))
self.assertTrue(dt.temporal_pattern is None)
self.assertTrue(dt.time is None)
def test_discrete(self):
dt = equations.DiscreteEquation()
assert dt.parameters == {}
def test_discrete(self):
dt = equations.DiscreteEquation()
self.assertEqual(dt.parameters, {})
