The Virtual Brain Project

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creators Package

allen_creator

The adapters in this module create new connectivities from the Allen Institute data using their SDK.

class tvb.adapters.creators.allen_creator.AllenConnectomeBuilder[source]

Bases: tvb.core.adapters.abcadapter.ABCAsynchronous

Handler for uploading a mouse connectivity from Allen dataset using AllenSDK.

RESOLUTION_OPTIONS = [{'name': '25', 'value': '25'}, {'name': '50', 'value': '50'}, {'name': '100', 'value': '100'}]
WEIGHTS_OPTIONS = [{'name': '(projection density)/(injection density)', 'value': '1'}, {'name': 'projection density', 'value': '2'}, {'name': 'projection energy', 'value': '3'}]
get_input_tree()[source]
get_output()[source]
get_required_disk_size(**kwargs)[source]
get_required_memory_size(**kwargs)[source]
launch(resolution, weighting, inf_vox_thresh, vol_thresh)[source]
tvb.adapters.creators.allen_creator.AreasVolumeTreshold(tvb_mcc, projmaps, vol_thresh, resolution, Vol, ontology)[source]
tvb.adapters.creators.allen_creator.AreasVoxelTreshold(tvb_mcc, projmaps, inf_vox_thresh, Vol, ontology)[source]
tvb.adapters.creators.allen_creator.ConstructTractLengths(centres)[source]
tvb.adapters.creators.allen_creator.Construct_centres(tvb_mcc, ontology, order, key_ord)[source]
tvb.adapters.creators.allen_creator.ConstructingSC(projmaps, order, key_ord)[source]
tvb.adapters.creators.allen_creator.CreateFileOrder(projmaps, ontology)[source]
tvb.adapters.creators.allen_creator.DictionaireBuilder(tvb_mcc, TransgenicLine)[source]
tvb.adapters.creators.allen_creator.DownloadAndConstructMatrix(tvb_mcc, weighting, ist2e, TransgenicLine)[source]
tvb.adapters.creators.allen_creator.MouseBrainVisualizer(Vol, order, key_ord, unique_parents, unique_grandparents, ontology, projmaps)[source]
tvb.adapters.creators.allen_creator.ParentsAndGrandParentsFinder(tvb_mcc, order, key_ord, ontology)[source]
tvb.adapters.creators.allen_creator.RotateReference(allen)[source]
tvb.adapters.creators.allen_creator.pmsCleaner(projmaps)[source]

connectivity_creator

class tvb.adapters.creators.connectivity_creator.ConnectivityCreator[source]

Bases: tvb.core.adapters.abcadapter.ABCAsynchronous

This adapter creates a Connectivity.

get_input_tree()[source]
get_output()[source]
get_required_disk_size(original_connectivity, new_weights, new_tracts, interest_area_indexes, **kwargs)[source]
get_required_memory_size(**_)[source]
launch(original_connectivity, new_weights, new_tracts, interest_area_indexes, **kwargs)[source]

Method to be called when user submits changes on the Connectivity matrix in the Visualizer.

local_connectivity_creator

class tvb.adapters.creators.local_connectivity_creator.LocalConnectivityCreator[source]

Bases: tvb.core.adapters.abcadapter.ABCAsynchronous

The purpose of this adapter is create a LocalConnectivity.

get_input_tree()[source]

Returns the input interface for this adapter.

get_lconn_equation(kwargs)[source]

Get the equation for the local connectivity from a dictionary of arguments.

get_output()[source]

Describes the outputs of the launch method.

get_required_disk_size(**kwargs)[source]

Returns the required disk size to be able to run the adapter. (in kB)

get_required_memory_size(**kwargs)[source]

Return the required memory to run this algorithm.

launch(**kwargs)[source]

Used for creating a LocalConnectivity

stimulus_creator

class tvb.adapters.creators.stimulus_creator.RegionStimulusCreator[source]

Bases: tvb.core.adapters.abcadapter.ABCSynchronous

The purpose of this adapter is to create a StimuliRegion.

get_input_tree()[source]

Returns the input interface for this adapter.

get_output()[source]

Describes the outputs of the launch method.

get_required_disk_size(**kwargs)[source]

Returns the required disk size to be able to run the adapter. (in kB)

get_required_memory_size(**kwargs)[source]

Return the required memory to run this algorithm.

launch(**kwargs)[source]

Used for creating a StimuliRegion instance

class tvb.adapters.creators.stimulus_creator.SurfaceStimulusCreator[source]

Bases: tvb.core.adapters.abcadapter.ABCSynchronous

The purpose of this adapter is to create a StimuliSurface.

get_input_tree()[source]

Returns the input interface for this adapter.

get_output()[source]

Describes the outputs of the launch method.

get_required_disk_size(**kwargs)[source]

Returns the required disk size to be able to run the adapter. (in kB)

get_required_memory_size(**kwargs)[source]

Return the required memory to run this algorithm.

get_spatial_equation(kwargs)[source]

From a dictionary of arguments build the spatial equation.

get_temporal_equation(kwargs)[source]

From a dictionary of arguments build the temporal equation.

launch(**kwargs)[source]

Used for creating a StimuliSurface instance