class SensorsData(MappedType):
"""
Base Sensors class.
All sensors have locations.
Some will have orientations, e.g. MEG.
"""
_ui_name = "Unknown sensors"
sensors_type = basic.String
__mapper_args__ = {'polymorphic_on': 'sensors_type'}
default = readers.File(
folder_path="sensors",
file_name='EEG_unit_vectors_BrainProducts_62.txt.bz2')
labels = arrays.StringArray(label="Sensor labels",
console_default=default.read_data(
usecols=(0, ),
dtype="string",
field="labels"))
locations = arrays.PositionArray(label="Sensor locations",
console_default=default.read_data(
usecols=(1, 2, 3), field="locations"))
has_orientation = basic.Bool(default=False)
orientations = arrays.OrientationArray(required=False)
number_of_sensors = basic.Integer(
label="Number of sensors",
doc="""The number of sensors described by these Sensors.""")
def test_cortexdata(self):
dt = surfaces.Cortex()
## Initialize Local Connectivity, to avoid long computation time.
reader = readers.File(folder_path="surfaces/cortex_reg13")
dt.local_connectivity = surfaces.LocalConnectivity()
dt.local_connectivity.matrix = reader.read_data("nearest_neighbour.mat", "LocalCoupling")
dt.configure()
summary_info = dt.summary_info
self.assertTrue(abs(summary_info['Region area, maximum (mm:math:`^2`)'] - 9119.4540365252615) < 0.00000001)
self.assertTrue(abs(summary_info['Region area, mean (mm:math:`^2`)'] - 3366.2542250541251) < 0.00000001)
self.assertTrue(abs(summary_info['Region area, minimum (mm:math:`^2`)'] - 366.48271886512993) < 0.00000001)
self.assertEqual(dt.get_data_shape('vertices'), (16384, 3))
self.assertEqual(dt.get_data_shape('vertex_normals'), (16384, 3))
self.assertEqual(dt.get_data_shape('triangles'), (32760, 3))
class RegionMappingData(arrays.MappedArray):
"""
An array representing a measure of a Connectivity dataType.
"""
default = readers.File(folder_path="surfaces/cortex_reg13")
array_data = arrays.IndexArray(
console_default=default.read_data(file_name="o52r00_irp2008.txt.bz2",
dtype=numpy.int32,
field="array_data"))
connectivity = Connectivity
surface = SurfaceData
__generate_table__ = True
class ConnectivityData(MappedType):
"""
This class primarily exists to bundle the long range structural connectivity
data into a single object.
"""
default = readers.File(folder_path="connectivity/o52r00_irp2008")
parcellation_mask = volumes.ParcellationMask(
label="Parcellation mask (volume)",
required=False,
doc=
"""A 3D volume mask defining the parcellation of the brain into distinct regions."""
)
region_labels = arrays.StringArray(
label="Region labels",
console_default=default.read_data(file_name="centres.txt.bz2",
usecols=(0, ),
dtype="string",
field="region_labels"),
doc=
"""Short strings, 'labels', for the regions represented by the connectivity matrix."""
)
weights = arrays.FloatArray(
label="Connection strengths",
console_default=default.read_data(file_name="weights.txt.bz2",
field="weights"),
doc=
"""Matrix of values representing the strength of connections between regions, arbitrary units."""
)
unidirectional = basic.Integer(
default=0,
required=False,
doc=
"1, when the weights matrix is square and symmetric over the main diagonal, 0 when bi-directional matrix."
)
tract_lengths = arrays.FloatArray(
label="Tract lengths",
console_default=default.read_data(file_name="tract_lengths.txt.bz2",
field="tract_lengths"),
doc="""The length of myelinated fibre tracts between regions.
If not provided Euclidean distance between region centres is used.""")
speed = arrays.FloatArray(
label="Conduction speed",
default=numpy.array([3.0]),
file_storage=core.FILE_STORAGE_NONE,
doc=
"""A single number or matrix of conduction speeds for the myelinated fibre tracts between regions."""
)
centres = arrays.PositionArray(
label="Region centres",
console_default=default.read_data(file_name="centres.txt.bz2",
usecols=(1, 2, 3),
field="centres"),
doc="An array specifying the location of the centre of each region.")
cortical = arrays.BoolArray(
label="Cortical",
console_default=default.read_data(file_name="cortical.txt.bz2",
dtype=numpy.bool,
field="cortical"),
required=False,
doc=
"""A boolean vector specifying whether or not a region is part of the cortex."""
)
hemispheres = arrays.BoolArray(
label="Hemispheres (True for Right and False for Left Hemisphere",
required=False,
doc=
"""A boolean vector specifying whether or not a region is part of the right hemisphere"""
)
orientations = arrays.OrientationArray(
label="Average region orientation",
console_default=default.read_data(
file_name="average_orientations.txt.bz2", field="orientations"),
required=False,
doc=
"""Unit vectors of the average orientation of the regions represented in the connectivity matrix.
NOTE: Unknown data should be zeros.""")
areas = arrays.FloatArray(
label="Area of regions",
console_default=default.read_data(file_name="areas.txt.bz2",
field="areas"),
required=False,
doc=
"""Estimated area represented by the regions in the connectivity matrix.
NOTE: Unknown data should be zeros.""")
idelays = arrays.IndexArray(
label="Conduction delay indices",
required=False,
file_storage=core.FILE_STORAGE_NONE,
doc="An array of time delays between regions in integration steps.")
delays = arrays.FloatArray(
label="Conduction delay",
file_storage=core.FILE_STORAGE_NONE,
required=False,
doc=
"""Matrix of time delays between regions in physical units, setting conduction speed automatically
combines with tract lengths to update this matrix, i.e. don't try and change it manually."""
)
number_of_regions = basic.Integer(
label="Number of regions",
doc="""The number of regions represented in this Connectivity """)
# ------------- FRAMEWORK ATTRIBUTES -----------------------------
# Rotation if positions are not normalized.
nose_correction = basic.JSONType(required=False)
# Original Connectivity, from which current connectivity was edited.
parent_connectivity = basic.String(required=False)
# In case of edited Connectivity, this are the nodes left in interest area,
# the rest were part of a lesion, so they were removed.
saved_selection = basic.JSONType(required=False)
class SurfaceData(MappedType):
"""
This class primarily exists to bundle the structural Surface data into a
single object.
"""
default = readers.File(folder_path="surfaces/cortex_reg13")
vertices = arrays.PositionArray(
label="Vertex positions",
order=-1,
console_default=default.read_data(file_name="vertices.txt.bz2",
field="vertices"),
doc="""An array specifying coordinates for the surface vertices.""")
triangles = arrays.IndexArray(
label="Triangles",
order=-1,
target=vertices,
console_default=default.read_data(file_name="triangles.txt.bz2",
dtype=numpy.int32,
field="triangles"),
doc=
"""Array of indices into the vertices, specifying the triangles which define the surface."""
)
vertex_normals = arrays.OrientationArray(
label="Vertex normal vectors",
order=-1,
console_default=default.read_data(file_name="vertex_normals.txt.bz2",
field="vertex_normals"),
doc="""An array of unit normal vectors for the surfaces vertices.""")
triangle_normals = arrays.OrientationArray(
label="Triangle normal vectors",
order=-1,
doc="""An array of unit normal vectors for the surfaces triangles.""")
geodesic_distance_matrix = SparseMatrix(
label="Geodesic distance matrix",
order=-1,
required=False,
file_storage=FILE_STORAGE_NONE,
doc="""A sparse matrix of truncated geodesic distances""") # 'CS'
number_of_vertices = basic.Integer(
label="Number of vertices",
order=-1,
doc="""The number of vertices making up this surface.""")
number_of_triangles = basic.Integer(
label="Number of triangles",
order=-1,
doc="""The number of triangles making up this surface.""")
##--------------------- FRAMEWORK ATTRIBUTES -----------------------------##
hemisphere_mask = arrays.BoolArray(
label="An array specifying if a vertex belongs to the right hemisphere",
file_storage=FILE_STORAGE_NONE,
required=False,
order=-1)
zero_based_triangles = basic.Bool(order=-1)
split_triangles = arrays.IndexArray(order=-1, required=False)
number_of_split_slices = basic.Integer(order=-1)
split_slices = basic.Dict(order=-1)
bi_hemispheric = basic.Bool(order=-1)
surface_type = basic.String
__mapper_args__ = {'polymorphic_on': 'surface_type'}