The adapters in this module create new connectivities from the Allen Institute data using their SDK.
Bases: tvb.core.neotraits.view_model.ViewModel
weighting : tvb.adapters.creators.allen_creator.AllenConnectModel.weighting = Int(field_type=<class ‘int’>, default=1, required=True)
operation_group_gid : tvb.core.neotraits.view_model.ViewModel.operation_group_gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
ranges : tvb.core.neotraits.view_model.ViewModel.ranges = Attr(field_type=<class ‘str’>, default=None, required=False)
range_values : tvb.core.neotraits.view_model.ViewModel.range_values = Attr(field_type=<class ‘str’>, default=None, required=False)
is_metric_operation : tvb.core.neotraits.view_model.ViewModel.is_metric_operation = Attr(field_type=<class ‘bool’>, default=False, required=True)
gid : tvb.basic.neotraits._core.HasTraits.gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
Declares a float. This is different from Attr(field_type=float). The former enforces float subtypes. This allows any type that can be safely cast to the declared float type according to numpy rules.
Reading and writing this attribute is slower than a plain python attribute. In performance sensitive code you might want to use plain python attributes or even better local variables.
Declares an integer This is different from Attr(field_type=int). The former enforces int subtypes This allows all integer types, including numpy ones that can be safely cast to the declared type according to numpy rules
Declares a float. This is different from Attr(field_type=float). The former enforces float subtypes. This allows any type that can be safely cast to the declared float type according to numpy rules.
Reading and writing this attribute is slower than a plain python attribute. In performance sensitive code you might want to use plain python attributes or even better local variables.
Declares an integer This is different from Attr(field_type=int). The former enforces int subtypes This allows all integer types, including numpy ones that can be safely cast to the declared type according to numpy rules
Bases: tvb.core.adapters.abcadapter.ABCAdapter
Handler for uploading a mouse connectivity from Allen dataset using AllenSDK.
the method includes in the parcellation only brain regions whose volume is greater than vol_thresh
the method creates file order and keyord that will be the link between the structural conn order and the id key in the Allen database
the method returns a volume indexed between 0 and N-1, with N=tot brain areas in the parcellation. -1=background and areas that are not in the parcellation
Bases: tvb.core.adapters.abcadapter.ABCAdapter
This adapter creates a Connectivity.
Bases: tvb.core.neotraits.view_model.ViewModel
original_connectivity : tvb.adapters.creators.connectivity_creator.ConnectivityCreatorModel.original_connectivity = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
new_weights : tvb.adapters.creators.connectivity_creator.ConnectivityCreatorModel.new_weights = NArray(label=’Weights json array’, dtype=float64, default=None, dim_names=(), ndim=None, required=True)
new_tracts : tvb.adapters.creators.connectivity_creator.ConnectivityCreatorModel.new_tracts = NArray(label=’Tracts json array’, dtype=float64, default=None, dim_names=(), ndim=None, required=True)
interest_area_indexes : tvb.adapters.creators.connectivity_creator.ConnectivityCreatorModel.interest_area_indexes = NArray(label=’Indices of selected nodes as json array’, dtype=int64, default=None, dim_names=(), ndim=None, required=True)
is_branch : tvb.adapters.creators.connectivity_creator.ConnectivityCreatorModel.is_branch = Attr(field_type=<class ‘bool’>, default=None, required=False)
operation_group_gid : tvb.core.neotraits.view_model.ViewModel.operation_group_gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
ranges : tvb.core.neotraits.view_model.ViewModel.ranges = Attr(field_type=<class ‘str’>, default=None, required=False)
range_values : tvb.core.neotraits.view_model.ViewModel.range_values = Attr(field_type=<class ‘str’>, default=None, required=False)
is_metric_operation : tvb.core.neotraits.view_model.ViewModel.is_metric_operation = Attr(field_type=<class ‘bool’>, default=False, required=True)
gid : tvb.basic.neotraits._core.HasTraits.gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
Declares a numpy array. dtype enforces the dtype. The default dtype is float32. An optional symbolic shape can be given, as a tuple of Dim attributes from the owning class. The shape will be enforced, but no broadcasting will be done. domain declares what values are allowed in this array. It can be any object that can be checked for membership Defaults are checked if they are in the declared domain. For performance reasons this does not happen on every attribute set.
An Attr declares the following about the attribute it describes: * the type * a default value shared by all instances * if the value might be missing * documentation It will resolve to attributes on the instance.
Declares a numpy array. dtype enforces the dtype. The default dtype is float32. An optional symbolic shape can be given, as a tuple of Dim attributes from the owning class. The shape will be enforced, but no broadcasting will be done. domain declares what values are allowed in this array. It can be any object that can be checked for membership Defaults are checked if they are in the declared domain. For performance reasons this does not happen on every attribute set.
Declares a numpy array. dtype enforces the dtype. The default dtype is float32. An optional symbolic shape can be given, as a tuple of Dim attributes from the owning class. The shape will be enforced, but no broadcasting will be done. domain declares what values are allowed in this array. It can be any object that can be checked for membership Defaults are checked if they are in the declared domain. For performance reasons this does not happen on every attribute set.
Keep a GID but also link the type of DataType it should point to
Bases: tvb.core.adapters.abcadapter.ABCAdapter
The purpose of this adapter is create a LocalConnectivity.
Bases: tvb.core.adapters.abcadapter.ABCAdapterForm
Bases: tvb.core.neotraits.view_model.ViewModel, tvb.datatypes.local_connectivity.LocalConnectivity
surface : tvb.adapters.creators.local_connectivity_creator.LocalConnectivityCreatorModel.surface = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
display_name : tvb.adapters.creators.local_connectivity_creator.LocalConnectivityCreatorModel.display_name = Str(field_type=<class ‘str’>, default=None, required=False)
operation_group_gid : tvb.core.neotraits.view_model.ViewModel.operation_group_gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
ranges : tvb.core.neotraits.view_model.ViewModel.ranges = Attr(field_type=<class ‘str’>, default=None, required=False)
range_values : tvb.core.neotraits.view_model.ViewModel.range_values = Attr(field_type=<class ‘str’>, default=None, required=False)
is_metric_operation : tvb.core.neotraits.view_model.ViewModel.is_metric_operation = Attr(field_type=<class ‘bool’>, default=False, required=True)
matrix : tvb.datatypes.local_connectivity.LocalConnectivity.matrix = Attr(field_type=<class ‘scipy.sparse.base.spmatrix’>, default=None, required=False)
equation : tvb.datatypes.local_connectivity.LocalConnectivity.equation = Attr(field_type=<class ‘tvb.datatypes.equations.FiniteSupportEquation’>, default=<tvb.datatypes.equations.Gaussian object at 0x7f01487dc690>, required=False)
gid : tvb.basic.neotraits._core.HasTraits.gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
Keep a GID but also link the type of DataType it should point to
Bases: tvb.core.adapters.abcadapter.ABCAdapter
The purpose of this adapter is to create a StimuliRegion.
Returns the required disk size to be able to run the adapter. (in kB)
Bases: tvb.core.adapters.abcadapter.ABCAdapterForm
alias of PulseTrain
Bases: tvb.core.neotraits.view_model.ViewModel, tvb.datatypes.patterns.StimuliRegion
temporal : tvb.adapters.creators.stimulus_creator.RegionStimulusCreatorModel.temporal = Attr(field_type=<class ‘tvb.datatypes.equations.TemporalApplicableEquation’>, default=<tvb.datatypes.equations.PulseTrain object at 0x7f0088ebabd0>, required=True)
connectivity : tvb.adapters.creators.stimulus_creator.RegionStimulusCreatorModel.connectivity = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
display_name : tvb.adapters.creators.stimulus_creator.RegionStimulusCreatorModel.display_name = Str(field_type=<class ‘str’>, default=None, required=False)
operation_group_gid : tvb.core.neotraits.view_model.ViewModel.operation_group_gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
ranges : tvb.core.neotraits.view_model.ViewModel.ranges = Attr(field_type=<class ‘str’>, default=None, required=False)
range_values : tvb.core.neotraits.view_model.ViewModel.range_values = Attr(field_type=<class ‘str’>, default=None, required=False)
is_metric_operation : tvb.core.neotraits.view_model.ViewModel.is_metric_operation = Attr(field_type=<class ‘bool’>, default=False, required=True)
spatial : tvb.datatypes.patterns.StimuliRegion.spatial = Attr(field_type=<class ‘tvb.datatypes.equations.DiscreteEquation’>, default=<tvb.datatypes.equations.DiscreteEquation object at 0x7f01485c8310>, required=True)
weight : tvb.datatypes.patterns.StimuliRegion.weight = NArray(label=’scaling’, dtype=float64, default=None, dim_names=(), ndim=None, required=True)
gid : tvb.basic.neotraits._core.HasTraits.gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
Keep a GID but also link the type of DataType it should point to
An Attr declares the following about the attribute it describes: * the type * a default value shared by all instances * if the value might be missing * documentation It will resolve to attributes on the instance.
Bases: tvb.core.adapters.abcadapter.ABCAdapter
The purpose of this adapter is to create a StimuliSurface.
Returns the required disk size to be able to run the adapter. (in kB)
Bases: tvb.core.adapters.abcadapter.ABCAdapterForm
alias of Sigmoid
alias of PulseTrain
Bases: tvb.core.neotraits.view_model.ViewModel, tvb.datatypes.patterns.StimuliSurface
spatial : tvb.adapters.creators.stimulus_creator.SurfaceStimulusCreatorModel.spatial = Attr(field_type=<class ‘tvb.datatypes.equations.FiniteSupportEquation’>, default=<tvb.datatypes.equations.Sigmoid object at 0x7f008f569190>, required=True)
temporal : tvb.adapters.creators.stimulus_creator.SurfaceStimulusCreatorModel.temporal = Attr(field_type=<class ‘tvb.datatypes.equations.TemporalApplicableEquation’>, default=<tvb.datatypes.equations.PulseTrain object at 0x7f0088eba590>, required=True)
surface : tvb.adapters.creators.stimulus_creator.SurfaceStimulusCreatorModel.surface = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
display_name : tvb.adapters.creators.stimulus_creator.SurfaceStimulusCreatorModel.display_name = Str(field_type=<class ‘str’>, default=None, required=False)
operation_group_gid : tvb.core.neotraits.view_model.ViewModel.operation_group_gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
ranges : tvb.core.neotraits.view_model.ViewModel.ranges = Attr(field_type=<class ‘str’>, default=None, required=False)
range_values : tvb.core.neotraits.view_model.ViewModel.range_values = Attr(field_type=<class ‘str’>, default=None, required=False)
is_metric_operation : tvb.core.neotraits.view_model.ViewModel.is_metric_operation = Attr(field_type=<class ‘bool’>, default=False, required=True)
focal_points_triangles : tvb.datatypes.patterns.StimuliSurface.focal_points_triangles = NArray(label=’Focal points triangles’, dtype=int64, default=None, dim_names=(), ndim=None, required=True)
gid : tvb.basic.neotraits._core.HasTraits.gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
An Attr declares the following about the attribute it describes: * the type * a default value shared by all instances * if the value might be missing * documentation It will resolve to attributes on the instance.
Keep a GID but also link the type of DataType it should point to
An Attr declares the following about the attribute it describes: * the type * a default value shared by all instances * if the value might be missing * documentation It will resolve to attributes on the instance.