visualizers
Package¶
List here all Python modules where Visualization adapters are described. Listed modules will be introspected and DB filled.
annotations_viewer
¶
- class tvb.adapters.visualizers.annotations_viewer.ConnectivityAnnotationsView[source]¶
Bases:
ABCSurfaceDisplayer
Given a Connectivity Matrix and a Surface data the viewer will display the matrix ‘inside’ the surface data. The surface is only displayed as a shadow.
- get_required_memory_size(view_model: ConnectivityAnnotationsViewModel) int [source]¶
Abstract method to be implemented in each adapter. Should return the required memory for launching the adapter.
- get_triangles_mapping(region_mapping_gid)[source]¶
:return Numpy array of length triangles and for each the region corresponding to one of its vertices.
- launch(view_model: ConnectivityAnnotationsViewModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.annotations_viewer.ConnectivityAnnotationsViewForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.annotations_viewer.ConnectivityAnnotationsViewModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.annotations_viewer.ConnectivityAnnotationsViewModel]¶
Attributes declared¶
connectivity_index : tvb.adapters.visualizers.annotations_viewer.ConnectivityAnnotationsViewModel.connectivity_index = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
annotations_index : tvb.adapters.visualizers.annotations_viewer.ConnectivityAnnotationsViewModel.annotations_index = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
- region_mapping_indextvb.adapters.visualizers.annotations_viewer.ConnectivityAnnotationsViewModel.region_mapping_index = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
A region map to identify us the Cortical Surface to display, as well as how the mapping from Connectivity to Cortex is done
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)
- annotations_index¶
Keep a GID but also link the type of DataType it should point to
- connectivity_index¶
Keep a GID but also link the type of DataType it should point to
- region_mapping_index¶
Keep a GID but also link the type of DataType it should point to
brain
¶
- class tvb.adapters.visualizers.brain.BrainViewer[source]¶
Bases:
ABCSurfaceDisplayer
Interface between the 3D view of the Brain Cortical Surface and TVB framework. This viewer will build the required parameter dictionary that will be sent to the HTML / JS for further processing, having as end result a brain surface plus activity that will be displayed in 3D.
- PAGE_SIZE = 500¶
- compute_parameters(time_series, shell_surface=None)[source]¶
Create the required parameter dictionary for the HTML/JS viewer.
- Return type:
dict
- Raises:
Exception – when * number of measure points exceeds the maximum allowed * a Face object cannot be found in database
- get_required_memory_size(view_model: BrainViewerModel) ndarray [source]¶
Assume one page doesn’t get ‘dumped’ in time and it is highly probably that two consecutive pages will be in the same time in memory.
- launch(view_model: BrainViewerModel) dict [source]¶
Build visualizer’s page.
- class tvb.adapters.visualizers.brain.BrainViewerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.brain.BrainViewerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.brain.BrainViewerModel]¶
Attributes declared¶
time_series : tvb.adapters.visualizers.brain.BrainViewerModel.time_series = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
- shell_surfacetvb.adapters.visualizers.brain.BrainViewerModel.shell_surface = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
Surface to be displayed semi-transparently as overlay, for visual navigation purposes only.
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)
- shell_surface¶
Keep a GID but also link the type of DataType it should point to
- time_series¶
Keep a GID but also link the type of DataType it should point to
- class tvb.adapters.visualizers.brain.DualBrainViewer[source]¶
Bases:
BrainViewer
Visualizer merging Brain 3D display and EEG lines display.
- launch(view_model: DualBrainViewerModel) dict [source]¶
Build visualizer’s page.
- populate_surface_fields(time_series_index)[source]¶
Prepares the urls from which the client may read the data needed for drawing the surface.
- class tvb.adapters.visualizers.brain.DualBrainViewerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.brain.DualBrainViewerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.brain.DualBrainViewerModel]¶
Attributes declared¶
time_series : tvb.adapters.visualizers.brain.DualBrainViewerModel.time_series = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
- projection_surfacetvb.adapters.visualizers.brain.DualBrainViewerModel.projection_surface = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
A surface on which to project the results. When missing, the first EEGCap is taken. This parameter is ignored when InternalSensors measures.
- shell_surfacetvb.adapters.visualizers.brain.DualBrainViewerModel.shell_surface = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
Wrapping surface over the internal sensors, to be displayed semi-transparently, for visual purposes only.
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)
- projection_surface¶
Keep a GID but also link the type of DataType it should point to
- shell_surface¶
Keep a GID but also link the type of DataType it should point to
- time_series¶
Keep a GID but also link the type of DataType it should point to
complex_imaginary_coherence
¶
- class tvb.adapters.visualizers.complex_imaginary_coherence.ImaginaryCoherenceDisplay[source]¶
Bases:
ABCDisplayer
This viewer takes as inputs a result from complex coherence analysis, and returns required parameters for a MatplotLib representation.
- get_required_memory_size(view_model: ImaginaryCoherenceDisplayModel) ndarray [source]¶
Return the required memory to run this algorithm.
- launch(view_model: ImaginaryCoherenceDisplayModel) dict [source]¶
Draw interactive display.
- class tvb.adapters.visualizers.complex_imaginary_coherence.ImaginaryCoherenceDisplayForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.complex_imaginary_coherence.ImaginaryCoherenceDisplayModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.complex_imaginary_coherence.ImaginaryCoherenceDisplayModel]¶
Attributes declared¶
- input_datatvb.adapters.visualizers.complex_imaginary_coherence.ImaginaryCoherenceDisplayModel.input_data = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
Imaginary Coherence Analysis to display
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)
- input_data¶
Keep a GID but also link the type of DataType it should point to
connectivity
¶
- class tvb.adapters.visualizers.connectivity.Connectivity2DViewer[source]¶
Bases:
object
Having as inputs a Connectivity matrix(required) and two arrays that represent the colors and shapes of the nodes from the matrix(optional) the viewer will build the required parameter dictionary that will be sent to the HTML/JS 2D representation of the connectivity matrix.
- DEFAULT_COLOR = '#d73027'¶
- MAX_RAY = 40¶
- MAX_WEIGHT_VALUE = 0.6¶
- MIN_RAY = 4¶
- MIN_WEIGHT_VALUE = 0.0¶
- OTHER_COLOR = '#1a9850'¶
- compute_parameters(input_data, colors=None, rays=None, step=None)[source]¶
Build the required HTML response to be displayed.
- Raises:
LaunchException – when number of regions in input_data is less than 3
- class tvb.adapters.visualizers.connectivity.Connectivity3DViewer[source]¶
Bases:
object
Behavior for the HTML/JS 3D representation of the connectivity matrix.
- static compute_parameters(input_data, colors=None, rays=None)[source]¶
Having as inputs a Connectivity matrix(required) and two arrays that represent the rays and colors of the nodes from the matrix(optional) this method will build the required parameter dictionary that will be sent to the HTML/JS 3D representation of the connectivity matrix.
- class tvb.adapters.visualizers.connectivity.ConnectivityViewer[source]¶
Bases:
ABCSpaceDisplayer
Given a Connectivity Matrix and a Surface data the viewer will display the matrix ‘inside’ the surface data. The surface is only displayed as a shadow.
- static get_connectivity_parameters(input_connectivity, project_name, op_id)[source]¶
Returns a dictionary which contains all the needed data for drawing a connectivity.
- get_required_memory_size(view_model: ConnectivityViewerModel) int [source]¶
Return the required memory to run this algorithm.
- launch(view_model: ConnectivityViewerModel) dict [source]¶
Given the input connectivity data and the surface data, build the HTML response to be displayed.
- class tvb.adapters.visualizers.connectivity.ConnectivityViewerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.connectivity.ConnectivityViewerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.connectivity.ConnectivityViewerModel]¶
- Attributes meaning:
connectivity: GID towards the Connectivity object which will be displayed surface_data: if provided, it is displayed as a shadow to give an idea of the connectivity position
relative to the full brain cortical surface
colors: used to establish a colormap for the nodes displayed in 2D Connectivity viewers rays: used to establish the size of the spheres representing each node in 3D Nodes viewer step: a threshold applied to the 2D Connectivity Viewers to differentiate 2 types of nodes the ones
with a value greater that this will be displayed as red discs, instead of yellow
Attributes declared¶
connectivity : tvb.adapters.visualizers.connectivity.ConnectivityViewerModel.connectivity = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
- surface_datatvb.adapters.visualizers.connectivity.ConnectivityViewerModel.surface_data = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
The Brain Surface is used to give you an idea of the connectivity position relative to the full brain cortical surface. This surface will be displayed as a shadow (only used in 3D Edges tab).
- steptvb.adapters.visualizers.connectivity.ConnectivityViewerModel.step = Attr(field_type=<class ‘float’>, default=None, required=False)
All nodes with a value greater or equal (>=) than this threshold will be displayed as red discs, otherwise (<) they will be yellow. (This applies to 2D Connectivity tabs and the threshold will depend on the metric used to set the Node Color)
- colorstvb.adapters.visualizers.connectivity.ConnectivityViewerModel.colors = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
A ConnectivityMeasure DataType that establishes a colormap for the nodes displayed in the 2D Connectivity tabs.
- raystvb.adapters.visualizers.connectivity.ConnectivityViewerModel.rays = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
A ConnectivityMeasure datatype used to establish the size of the spheres representing each node. (It only applies to 3D Nodes tab).
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)
- colors¶
Keep a GID but also link the type of DataType it should point to
- connectivity¶
Keep a GID but also link the type of DataType it should point to
- rays¶
Keep a GID but also link the type of DataType it should point to
- step¶
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.
- surface_data¶
Keep a GID but also link the type of DataType it should point to
connectivity_edge_bundle
¶
A Javascript displayer for connectivity, using hierarchical edge bundle diagrams from d3.js.
- class tvb.adapters.visualizers.connectivity_edge_bundle.ConnectivityEdgeBundle[source]¶
Bases:
ABCDisplayer
- class tvb.adapters.visualizers.connectivity_edge_bundle.ConnectivityEdgeBundleForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.connectivity_edge_bundle.ConnectivityEdgeBundleModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.connectivity_edge_bundle.ConnectivityEdgeBundleModel]¶
Attributes declared¶
connectivity : tvb.adapters.visualizers.connectivity_edge_bundle.ConnectivityEdgeBundleModel.connectivity = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, 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)
- connectivity¶
Keep a GID but also link the type of DataType it should point to
cross_coherence
¶
A displayer for the cross coherence of a time series.
- class tvb.adapters.visualizers.cross_coherence.CrossCoherenceVisualizer[source]¶
Bases:
ABCMappedArraySVGVisualizer
- launch(view_model: CrossCoherenceVisualizerModel) dict [source]¶
Construct data for visualization and launch it.
- class tvb.adapters.visualizers.cross_coherence.CrossCoherenceVisualizerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.cross_coherence.CrossCoherenceVisualizerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.cross_coherence.CrossCoherenceVisualizerModel]¶
Attributes declared¶
datatype : tvb.adapters.visualizers.cross_coherence.CrossCoherenceVisualizerModel.datatype = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, 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)
- datatype¶
Keep a GID but also link the type of DataType it should point to
cross_correlation
¶
A visualizer for cross correlation.
- class tvb.adapters.visualizers.cross_correlation.CrossCorrelationVisualizer[source]¶
Bases:
ABCMappedArraySVGVisualizer
- launch(view_model: CrossCorrelationVisualizerModel) dict [source]¶
Construct data for visualization and launch it.
- class tvb.adapters.visualizers.cross_correlation.CrossCorrelationVisualizerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.cross_correlation.CrossCorrelationVisualizerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.cross_correlation.CrossCorrelationVisualizerModel]¶
Attributes declared¶
datatype : tvb.adapters.visualizers.cross_correlation.CrossCorrelationVisualizerModel.datatype = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, 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)
- datatype¶
Keep a GID but also link the type of DataType it should point to
eeg_monitor
¶
- class tvb.adapters.visualizers.eeg_monitor.EegMonitor[source]¶
Bases:
ABCSpaceDisplayer
This viewer takes as inputs at least one ArrayWrapper and at most 3 ArrayWrappers, and returns the needed parameters for a 2D representation of the values from these arrays, in EEG form. So far arrays of at most 3 dimensions are supported.
- compute_parameters(input_data, data_2=None, data_3=None, is_preview=False, is_extended_view=False, selected_dimensions=None)[source]¶
Start the JS visualizer, similar to EEG-lab
- Parameters:
is_preview – Boolean True wne shown on Burst page
selected_dimensions – from GUI int
is_extended_view – Boolean when to display as dual-viewer
input_data (TimeSeriesEEG) – Time series to display
data_2 – additional input data
data_3 – additional input data
- Returns:
the needed parameters for a 2D representation
- Return type:
dict
- Raises:
LaunchException – when at least two input data parameters are provided and they sample periods differ
- current_page = 0¶
- get_required_memory_size(view_model: EegMonitorModel) int [source]¶
Return the required memory to run this algorithm.
- has_nan = False¶
- launch(view_model: EegMonitorModel) dict [source]¶
Compute visualizer’s page
- page_size = 4000¶
- preview_page_size = 250¶
- class tvb.adapters.visualizers.eeg_monitor.EegMonitorForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.eeg_monitor.EegMonitorModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.eeg_monitor.EegMonitorModel]¶
Attributes declared¶
- input_datatvb.adapters.visualizers.eeg_monitor.EegMonitorModel.input_data = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
Time series to display.
- data_2tvb.adapters.visualizers.eeg_monitor.EegMonitorModel.data_2 = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
Time series to display.
- data_3tvb.adapters.visualizers.eeg_monitor.EegMonitorModel.data_3 = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
Time series to display.
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)
- data_2¶
Keep a GID but also link the type of DataType it should point to
- data_3¶
Keep a GID but also link the type of DataType it should point to
- input_data¶
Keep a GID but also link the type of DataType it should point to
fourier_spectrum
¶
- class tvb.adapters.visualizers.fourier_spectrum.FourierSpectrumDisplay[source]¶
Bases:
ABCDisplayer
This viewer takes as inputs a result form FFT analysis, and returns required parameters for a MatplotLib representation.
- get_required_memory_size(view_model: FourierSpectrumModel) dict [source]¶
Return the required memory to run this algorithm.
- launch(view_model: FourierSpectrumModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.fourier_spectrum.FourierSpectrumForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.fourier_spectrum.FourierSpectrumModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.fourier_spectrum.FourierSpectrumModel]¶
Attributes declared¶
- input_datatvb.adapters.visualizers.fourier_spectrum.FourierSpectrumModel.input_data = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
Fourier Analysis to display
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)
- input_data¶
Keep a GID but also link the type of DataType it should point to
histogram
¶
- class tvb.adapters.visualizers.histogram.HistogramViewer[source]¶
Bases:
ABCDisplayer
The viewer takes as input a result DataType as computed by BCT analyzers.
- get_required_memory_size(view_model: HistogramViewerModel) ndarray [source]¶
Return the required memory to run this algorithm.
- launch(view_model: HistogramViewerModel) dict [source]¶
Prepare input data for display.
- Parameters:
input_data (ConnectivityMeasureIndex) – A BCT computed measure for a Connectivity
- class tvb.adapters.visualizers.histogram.HistogramViewerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.histogram.HistogramViewerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.histogram.HistogramViewerModel]¶
Attributes declared¶
- input_datatvb.adapters.visualizers.histogram.HistogramViewerModel.input_data = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
A BCT computed measure for a Connectivity
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)
- input_data¶
Keep a GID but also link the type of DataType it should point to
ica
¶
A matrix visualizer for the Independent Component Analysis. It displays the mixing matrix of size n_features x n_components
- class tvb.adapters.visualizers.ica.ICA[source]¶
Bases:
ABCMappedArraySVGVisualizer
- class tvb.adapters.visualizers.ica.ICAForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.ica.ICAModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.ica.ICAModel]¶
Attributes declared¶
datatype : tvb.adapters.visualizers.ica.ICAModel.datatype = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
i_svar : tvb.adapters.visualizers.ica.ICAModel.i_svar = Attr(field_type=<class ‘int’>, default=0, required=True)
i_mode : tvb.adapters.visualizers.ica.ICAModel.i_mode = Attr(field_type=<class ‘int’>, default=0, 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)
- datatype¶
Keep a GID but also link the type of DataType it should point to
- i_mode¶
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.
- i_svar¶
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.
local_connectivity_view
¶
- class tvb.adapters.visualizers.local_connectivity_view.LocalConnectivityViewer[source]¶
Bases:
ABCDisplayer
Local connectivity visualizer
- get_required_memory_size()[source]¶
Abstract method to be implemented in each adapter. Should return the required memory for launching the adapter.
- launch(view_model)[source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.local_connectivity_view.LocalConnectivityViewerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.local_connectivity_view.LocalConnectivityViewerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.local_connectivity_view.LocalConnectivityViewerModel]¶
Attributes declared¶
local_conn : tvb.adapters.visualizers.local_connectivity_view.LocalConnectivityViewerModel.local_conn = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, 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)
- local_conn¶
Keep a GID but also link the type of DataType it should point to
matrix_viewer
¶
- class tvb.adapters.visualizers.matrix_viewer.ABCMappedArraySVGVisualizer[source]¶
Bases:
ABCSpaceDisplayer
To be inherited by visualizers for DataTypeMatrix subclasses
- compute_2d_view(dtm_index: DataTypeMatrix, slice_s: str)[source]¶
Create a 2d view of the matrix using the suggested slice If the given slice is invalid or fails to produce a 2d array the default is used which selects the first 2 dimensions. If the matrix is complex the real part is shown :param dtm_index: main input. It can have more then 2D :param slice_s: a string representation of a slice :return: (a 2d array, the slice used to make it, is_default_returned)
- static compute_raw_matrix_params(matrix)[source]¶
Serializes matrix data, shape and stride metadata to json
- extract_source_labels(datatype_matrix: DataTypeMatrix) list [source]¶
- get_required_memory_size(view_model: MatrixVisualizerModel) float [source]¶
Return required memory.
- class tvb.adapters.visualizers.matrix_viewer.MappedArrayVisualizer[source]¶
Bases:
ABCMappedArraySVGVisualizer
- launch(view_model: MatrixVisualizerModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.matrix_viewer.MatrixVisualizerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.matrix_viewer.MatrixVisualizerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.matrix_viewer.MatrixVisualizerModel]¶
Attributes declared¶
datatype : tvb.adapters.visualizers.matrix_viewer.MatrixVisualizerModel.datatype = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
slice : tvb.adapters.visualizers.matrix_viewer.MatrixVisualizerModel.slice = Attr(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)
gid : tvb.basic.neotraits._core.HasTraits.gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
- datatype¶
Keep a GID but also link the type of DataType it should point to
- slice¶
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.
pca
¶
A displayer for the principal component analysis.
- class tvb.adapters.visualizers.pca.PCA[source]¶
Bases:
ABCSpaceDisplayer
- class tvb.adapters.visualizers.pca.PCAForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.pca.PCAModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.pca.PCAModel]¶
Attributes declared¶
pca : tvb.adapters.visualizers.pca.PCAModel.pca = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, 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)
- pca¶
Keep a GID but also link the type of DataType it should point to
pearson_cross_correlation
¶
- class tvb.adapters.visualizers.pearson_cross_correlation.PearsonCorrelationCoefficientVisualizer[source]¶
Bases:
ABCMappedArraySVGVisualizer
Viewer for Pearson CorrelationCoefficients. Very similar to the CrossCorrelationVisualizer - this one done with Matplotlib
- class tvb.adapters.visualizers.pearson_cross_correlation.PearsonCorrelationCoefficientVisualizerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.pearson_cross_correlation.PearsonCorrelationCoefficientVisualizerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.pearson_cross_correlation.PearsonCorrelationCoefficientVisualizerModel]¶
Attributes declared¶
datatype : tvb.adapters.visualizers.pearson_cross_correlation.PearsonCorrelationCoefficientVisualizerModel.datatype = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, 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)
- datatype¶
Keep a GID but also link the type of DataType it should point to
pearson_edge_bundle
¶
- class tvb.adapters.visualizers.pearson_edge_bundle.PearsonEdgeBundle[source]¶
Bases:
ABCSpaceDisplayer
Viewer for Pearson CorrelationCoefficients. Very similar to the CrossCorrelationVisualizer - this one done with Matplotlib
- get_required_memory_size(view_model: PearsonCorrelationCoefficientVisualizerModel) ndarray [source]¶
Return required memory.
- launch(view_model: PearsonCorrelationCoefficientVisualizerModel) dict [source]¶
Construct data for visualization and launch it.
phase_plane_interactive
¶
- class tvb.adapters.visualizers.phase_plane_interactive.PhaseLineD3(model, integrator)[source]¶
Bases:
_PhaseSpace
- class tvb.adapters.visualizers.phase_plane_interactive.PhasePlane(model, integrator)[source]¶
Bases:
_PhaseSpace
Responsible with computing phase space slices and trajectories. A collection of math-y utilities it is view independent (holds no state related to views).
- class tvb.adapters.visualizers.phase_plane_interactive.PhasePlaneD3(model, integrator)[source]¶
Bases:
PhasePlane
Provides data for a d3 client
pse
¶
Data for Parameter Space Exploration view will be defined here. The purpose of this entities is to be used in Jinja2 UI, or for populating visualizer.
- class tvb.adapters.visualizers.pse.DiscretePSE(datatype_group_gid, color_metric, size_metric, back_page)[source]¶
Bases:
EnhancedDictionary
- class tvb.adapters.visualizers.pse.PSEDiscreteGroupModel(datatype_group_gid, color_metric, size_metric, back_page)[source]¶
Bases:
PSEGroupModel
- class tvb.adapters.visualizers.pse.PSEGroupModel(datatype_group_gid)[source]¶
Bases:
object
- property range1_values¶
- property range2_values¶
pse_discrete
¶
- class tvb.adapters.visualizers.pse_discrete.DiscretePSEAdapter[source]¶
Bases:
ABCDisplayer
Visualization adapter for Parameter Space Exploration. Will be used as a generic visualizer, accessible when input entity is DataTypeGroup. Will also be used in Burst as a supplementary navigation layer.
- get_required_memory_size(view_model: DiscretePSEAdapterModel) int [source]¶
Return the required memory to run this algorithm.
- launch(view_model: DiscretePSEAdapterModel) dict [source]¶
Launch the visualizer.
- class tvb.adapters.visualizers.pse_discrete.DiscretePSEAdapterForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.pse_discrete.DiscretePSEAdapterModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.pse_discrete.DiscretePSEAdapterModel]¶
Attributes declared¶
datatype_group : tvb.adapters.visualizers.pse_discrete.DiscretePSEAdapterModel.datatype_group = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, 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)
- datatype_group¶
Keep a GID but also link the type of DataType it should point to
pse_isocline
¶
- class tvb.adapters.visualizers.pse_isocline.IsoclinePSEAdapter[source]¶
Bases:
ABCDisplayer
Visualization adapter for Parameter Space Exploration. Will be used as a generic visualizer, accessible when input entity is DataTypeGroup. Will also be used in Burst as a supplementary navigation layer.
- burst_preview(view_model: IsoclinePSEAdapterModel) dict [source]¶
Generate the preview for the burst page.
- get_required_memory_size(view_model: IsoclinePSEAdapterModel) int [source]¶
Return the required memory to run this algorithm.
- launch(view_model)[source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.pse_isocline.IsoclinePSEAdapterForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.pse_isocline.IsoclinePSEAdapterModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.pse_isocline.IsoclinePSEAdapterModel]¶
Attributes declared¶
datatype_group : tvb.adapters.visualizers.pse_isocline.IsoclinePSEAdapterModel.datatype_group = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, 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)
- datatype_group¶
Keep a GID but also link the type of DataType it should point to
region_volume_mapping
¶
Backend-side for Visualizers that display measures on regions in the brain volume.
- class tvb.adapters.visualizers.region_volume_mapping.BaseVolumeVisualizerForm[source]¶
Bases:
ABCAdapterForm
- class tvb.adapters.visualizers.region_volume_mapping.BaseVolumeVisualizerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.region_volume_mapping.BaseVolumeVisualizerModel]¶
Attributes declared¶
background : tvb.adapters.visualizers.region_volume_mapping.BaseVolumeVisualizerModel.background = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, 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)
- background¶
Keep a GID but also link the type of DataType it should point to
- class tvb.adapters.visualizers.region_volume_mapping.ConnectivityMeasureVolumeVisualizer[source]¶
Bases:
_MappedArrayVolumeBase
- launch(view_model: ConnectivityMeasureVolumeVisualizerModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.region_volume_mapping.ConnectivityMeasureVolumeVisualizerForm[source]¶
Bases:
BaseVolumeVisualizerForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.region_volume_mapping.ConnectivityMeasureVolumeVisualizerModel(**kwargs)[source]¶
Bases:
BaseVolumeVisualizerModel
Traited class [tvb.adapters.visualizers.region_volume_mapping.ConnectivityMeasureVolumeVisualizerModel]¶
Attributes declared¶
- connectivity_measuretvb.adapters.visualizers.region_volume_mapping.ConnectivityMeasureVolumeVisualizerModel.connectivity_measure = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
A connectivity measure
region_mapping_volume : tvb.adapters.visualizers.region_volume_mapping.ConnectivityMeasureVolumeVisualizerModel.region_mapping_volume = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
background : tvb.adapters.visualizers.region_volume_mapping.BaseVolumeVisualizerModel.background = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, 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)
- connectivity_measure¶
Keep a GID but also link the type of DataType it should point to
- region_mapping_volume¶
Keep a GID but also link the type of DataType it should point to
- class tvb.adapters.visualizers.region_volume_mapping.MappedArrayVolumeVisualizer[source]¶
Bases:
_MappedArrayVolumeBase
This is a generic mapped array visualizer on a region volume. To view a multidimensional array one has to give this viewer a slice.
- launch(view_model: VolumeVisualizerModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.region_volume_mapping.MriVolumeVisualizer[source]¶
Bases:
_MappedArrayVolumeBase
- get_required_memory_size(view_model: BaseVolumeVisualizerModel) int [source]¶
Abstract method to be implemented in each adapter. Should return the required memory for launching the adapter.
- launch(view_model: BaseVolumeVisualizerModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.region_volume_mapping.MriVolumeVisualizerForm[source]¶
Bases:
BaseVolumeVisualizerForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.region_volume_mapping.RegionVolumeMappingVisualiser[source]¶
Bases:
_MappedArrayVolumeBase
- launch(view_model: RegionVolumeMappingVisualiserModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.region_volume_mapping.RegionVolumeMappingVisualiserForm[source]¶
Bases:
BaseVolumeVisualizerForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.region_volume_mapping.RegionVolumeMappingVisualiserModel(**kwargs)[source]¶
Bases:
BaseVolumeVisualizerModel
Traited class [tvb.adapters.visualizers.region_volume_mapping.RegionVolumeMappingVisualiserModel]¶
Attributes declared¶
region_mapping_volume : tvb.adapters.visualizers.region_volume_mapping.RegionVolumeMappingVisualiserModel.region_mapping_volume = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
- connectivity_measuretvb.adapters.visualizers.region_volume_mapping.RegionVolumeMappingVisualiserModel.connectivity_measure = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
A connectivity measure
background : tvb.adapters.visualizers.region_volume_mapping.BaseVolumeVisualizerModel.background = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, 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)
- connectivity_measure¶
Keep a GID but also link the type of DataType it should point to
- region_mapping_volume¶
Keep a GID but also link the type of DataType it should point to
- class tvb.adapters.visualizers.region_volume_mapping.VolumeVisualizerForm[source]¶
Bases:
BaseVolumeVisualizerForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.region_volume_mapping.VolumeVisualizerModel(**kwargs)[source]¶
Bases:
BaseVolumeVisualizerModel
Traited class [tvb.adapters.visualizers.region_volume_mapping.VolumeVisualizerModel]¶
Attributes declared¶
- measuretvb.adapters.visualizers.region_volume_mapping.VolumeVisualizerModel.measure = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
A measure to view on anatomy
region_mapping_volume : tvb.adapters.visualizers.region_volume_mapping.VolumeVisualizerModel.region_mapping_volume = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
data_slice : tvb.adapters.visualizers.region_volume_mapping.VolumeVisualizerModel.data_slice = Attr(field_type=<class ‘str’>, default=None, required=False)
background : tvb.adapters.visualizers.region_volume_mapping.BaseVolumeVisualizerModel.background = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, 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)
- data_slice¶
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.
- measure¶
Keep a GID but also link the type of DataType it should point to
- region_mapping_volume¶
Keep a GID but also link the type of DataType it should point to
sensors
¶
- class tvb.adapters.visualizers.sensors.SensorsViewer[source]¶
Bases:
ABCDisplayer
Sensor visualizer - for visual inspecting of TVB Sensors DataTypes.
- get_required_memory_size()[source]¶
Abstract method to be implemented in each adapter. Should return the required memory for launching the adapter.
- launch(view_model: SensorsViewerModel) dict [source]¶
Prepare visualizer parameters.
We support viewing all sensor types through a single viewer, so that a user doesn’t need to go back to the data-page, for loading a different type of sensor.
- class tvb.adapters.visualizers.sensors.SensorsViewerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.sensors.SensorsViewerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.sensors.SensorsViewerModel]¶
Attributes declared¶
- sensorstvb.adapters.visualizers.sensors.SensorsViewerModel.sensors = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
Internals sensors to view
- projection_surfacetvb.adapters.visualizers.sensors.SensorsViewerModel.projection_surface = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
A surface on which to project the results. When missing, the first EEGCap is taken. This parameter is ignored when InternalSensors are inspected
- shell_surfacetvb.adapters.visualizers.sensors.SensorsViewerModel.shell_surface = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
Wrapping surface over the internal sensors, to be displayed semi-transparently, for visual purposes only.
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)
- projection_surface¶
Keep a GID but also link the type of DataType it should point to
- sensors¶
Keep a GID but also link the type of DataType it should point to
- shell_surface¶
Keep a GID but also link the type of DataType it should point to
- tvb.adapters.visualizers.sensors.function_sensors_to_surface(sensors_gid, surface_to_map_gid)[source]¶
Map EEG sensors onto the head surface (skin-air).
EEG sensor locations are typically only given on a unit sphere, that is, they are effectively only identified by their orientation with respect to a coordinate system. This method is used to map these unit vector sensor “locations” to a specific location on the surface of the skin.
Assumes coordinate systems are aligned, i.e. common x,y,z and origin.
- tvb.adapters.visualizers.sensors.prepare_mapped_sensors_as_measure_points_params(sensors, eeg_cap=None, adapter_id=None)[source]¶
Compute sensors positions by mapping them to the
eeg_cap
surface Ifeeg_cap
is not specified the mapping will use a default EEGCal DataType in current project. If no default EEGCap is found, return sensors as they are (not projected)- Returns:
dictionary to be used in Viewers for rendering measure_points
- Return type:
dict
surface_view
¶
- class tvb.adapters.visualizers.surface_view.ABCSurfaceDisplayer[source]¶
Bases:
ABCSpaceDisplayer
- class tvb.adapters.visualizers.surface_view.BaseSurfaceViewerForm[source]¶
Bases:
ABCAdapterForm
- class tvb.adapters.visualizers.surface_view.BaseSurfaceViewerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.surface_view.BaseSurfaceViewerModel]¶
Attributes declared¶
- region_maptvb.adapters.visualizers.surface_view.BaseSurfaceViewerModel.region_map = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
A region map
- connectivity_measuretvb.adapters.visualizers.surface_view.BaseSurfaceViewerModel.connectivity_measure = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
A connectivity measure
- shell_surfacetvb.adapters.visualizers.surface_view.BaseSurfaceViewerModel.shell_surface = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
Face surface to be displayed semi-transparently, for orientation only.
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)
- connectivity_measure¶
Keep a GID but also link the type of DataType it should point to
- region_map¶
Keep a GID but also link the type of DataType it should point to
- shell_surface¶
Keep a GID but also link the type of DataType it should point to
- class tvb.adapters.visualizers.surface_view.ConnectivityMeasureOnSurfaceViewer[source]¶
Bases:
SurfaceViewer
This displays a connectivity measure on a surface via a RegionMapping It reuses almost everything from SurfaceViewer, but it make required another input param.
- launch(view_model: BaseSurfaceViewerModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.surface_view.ConnectivityMeasureOnSurfaceViewerForm[source]¶
Bases:
BaseSurfaceViewerForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.surface_view.RegionMappingViewer[source]¶
Bases:
SurfaceViewer
This is a viewer for RegionMapping DataTypes. It reuses almost everything from SurfaceViewer, but it make required another input param.
- launch(view_model: BaseSurfaceViewerModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.surface_view.RegionMappingViewerForm[source]¶
Bases:
BaseSurfaceViewerForm
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.surface_view.SurfaceURLGenerator[source]¶
Bases:
URLGenerator
- class tvb.adapters.visualizers.surface_view.SurfaceViewer[source]¶
Bases:
ABCSurfaceDisplayer
Static SurfaceData visualizer - for visual inspecting imported surfaces in TVB. Optionally it can display associated RegionMapping entities.
- get_required_memory_size(view_model)[source]¶
Abstract method to be implemented in each adapter. Should return the required memory for launching the adapter.
- launch(view_model: SurfaceViewerModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.surface_view.SurfaceViewerForm[source]¶
Bases:
BaseSurfaceViewerForm
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.surface_view.SurfaceViewerModel(**kwargs)[source]¶
Bases:
BaseSurfaceViewerModel
Traited class [tvb.adapters.visualizers.surface_view.SurfaceViewerModel]¶
Attributes declared¶
surface : tvb.adapters.visualizers.surface_view.SurfaceViewerModel.surface = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
- region_maptvb.adapters.visualizers.surface_view.BaseSurfaceViewerModel.region_map = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
A region map
- connectivity_measuretvb.adapters.visualizers.surface_view.BaseSurfaceViewerModel.connectivity_measure = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
A connectivity measure
- shell_surfacetvb.adapters.visualizers.surface_view.BaseSurfaceViewerModel.shell_surface = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
Face surface to be displayed semi-transparently, for orientation only.
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)
- surface¶
Keep a GID but also link the type of DataType it should point to
- title = 'Surface Visualizer'¶
time_series
¶
A Javascript displayer for time series, using SVG.
- class tvb.adapters.visualizers.time_series.ABCSpaceDisplayer[source]¶
Bases:
ABCDisplayer
- static build_params_for_selectable_connectivity(connectivity: Connectivity) dict [source]¶
- build_params_for_subselectable_ts(ts_h5)[source]¶
creates a template dict with the initial selection to be displayed in a time series viewer
- class tvb.adapters.visualizers.time_series.TimeSeriesDisplay[source]¶
Bases:
ABCSpaceDisplayer
- MAX_PREVIEW_DATA_LENGTH = 200¶
- get_required_memory_size(view_model: TimeSeriesModel) int [source]¶
Return required memory.
- launch(view_model: TimeSeriesModel) dict [source]¶
Construct data for visualization and launch it.
- class tvb.adapters.visualizers.time_series.TimeSeriesForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.time_series.TimeSeriesModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.time_series.TimeSeriesModel]¶
Attributes declared¶
time_series : tvb.adapters.visualizers.time_series.TimeSeriesModel.time_series = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, 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)
- time_series¶
Keep a GID but also link the type of DataType it should point to
time_series_volume
¶
Backend-side for TS Visualizer of TS Volume DataTypes.
- class tvb.adapters.visualizers.time_series_volume.TimeSeriesVolumeVisualiser[source]¶
Bases:
_MappedArrayVolumeBase
- get_required_memory_size(view_model: TimeSeriesVolumeVisualiserModel) int [source]¶
Return required memory.
- get_view_region(ts_h5, volume_rm_h5, from_idx, to_idx, x, y, z, var=0, mode=0)[source]¶
Retrieve 3 slices through the Volume TS, at the given X, y and Z coordinates, and in time [from_idx .. to_idx].
- Parameters:
ts_h5 – input TimeSeriesH5
volume_rm_h5 – input RegionVolumeMappingH5
from_idx – int This will be the limit on the first dimension (time)
to_idx – int Also limit on the first Dimension (time)
x_plane – int coordinate
y_plane – int coordinate
z_plane – int coordinate
- Returns:
An array of 3 Matrices 2D, each containing the values to display in planes xy, yz and xy.
- get_voxel_time_series(entity_gid, **kwargs)[source]¶
Retrieve for a given voxel (x,y,z) the entire timeline.
- Parameters:
x – int coordinate
y – int coordinate
z – int coordinate
- Returns:
A complex dictionary with information about current voxel. The main part will be a vector with all the values over time from the x,y,z coordinates.
- launch(view_model: TimeSeriesVolumeVisualiserModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.time_series_volume.TimeSeriesVolumeVisualiserForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.time_series_volume.TimeSeriesVolumeVisualiserModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.time_series_volume.TimeSeriesVolumeVisualiserModel]¶
Attributes declared¶
time_series : tvb.adapters.visualizers.time_series_volume.TimeSeriesVolumeVisualiserModel.time_series = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
background : tvb.adapters.visualizers.time_series_volume.TimeSeriesVolumeVisualiserModel.background = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, 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)
- background¶
Keep a GID but also link the type of DataType it should point to
- time_series¶
Keep a GID but also link the type of DataType it should point to
topographic
¶
- class tvb.adapters.visualizers.topographic.TopographicViewer[source]¶
Bases:
ABCDisplayer
Interface between TVB Framework and web display of a topography viewer.
- get_required_memory_size(view_model: TopographicViewerModel) int [source]¶
Return the required memory to run this algorithm.
- launch(view_model: TopographicViewerModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.topographic.TopographicViewerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.topographic.TopographicViewerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.topographic.TopographicViewerModel]¶
Attributes declared¶
- data_0tvb.adapters.visualizers.topographic.TopographicViewerModel.data_0 = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
Punctual values for each node in the connectivity matrix. This will give the colors of the resulting topographic image.
- data_1tvb.adapters.visualizers.topographic.TopographicViewerModel.data_1 = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
Comparative values
- data_2tvb.adapters.visualizers.topographic.TopographicViewerModel.data_2 = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
Comparative values
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)
- data_0¶
Keep a GID but also link the type of DataType it should point to
- data_1¶
Keep a GID but also link the type of DataType it should point to
- data_2¶
Keep a GID but also link the type of DataType it should point to
tract
¶
A tracts visualizer .. moduleauthor:: Mihai Andrei <mihai.andrei@codemart.ro>
- class tvb.adapters.visualizers.tract.TractViewer[source]¶
Bases:
ABCSpaceDisplayer
Tract visualizer
- get_required_memory_size(view_model: TractViewerModel) int [source]¶
Abstract method to be implemented in each adapter. Should return the required memory for launching the adapter.
- launch(view_model: TractViewerModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.tract.TractViewerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.tract.TractViewerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.tract.TractViewerModel]¶
Attributes declared¶
tracts : tvb.adapters.visualizers.tract.TractViewerModel.tracts = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
- shell_surfacetvb.adapters.visualizers.tract.TractViewerModel.shell_surface = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=False)
Surface to be displayed semi-transparently, for visual purposes only.
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)
- shell_surface¶
Keep a GID but also link the type of DataType it should point to
- tracts¶
Keep a GID but also link the type of DataType it should point to
wavelet_spectrogram
¶
Plot the power of a WaveletCoefficients object
- class tvb.adapters.visualizers.wavelet_spectrogram.WaveletSpectrogramVisualizer[source]¶
Bases:
ABCDisplayer
Plot the power of a WaveletCoefficients object using SVG an D3.
- get_required_memory_size(view_model: WaveletSpectrogramVisualizerModel) int [source]¶
Return the required memory to run this algorithm.
- launch(view_model: WaveletSpectrogramVisualizerModel) dict [source]¶
To be implemented in each Adapter. Will contain the logic of the Adapter. Takes a ViewModel with data, dependency direction is: Adapter -> Form -> ViewModel Any returned DataType will be stored in DB, by the Framework.
- Parameters:
view_model – the data model corresponding to the current adapter
- class tvb.adapters.visualizers.wavelet_spectrogram.WaveletSpectrogramVisualizerForm[source]¶
Bases:
ABCAdapterForm
- static get_filters()[source]¶
Should keep filters for the required_datatype. These filters are stored in DB at introspection time. :return: FilterChain
- static get_input_name()[source]¶
The Form’s input name for the required_datatype. Will be stored in DB at introspection time. :return: str
- class tvb.adapters.visualizers.wavelet_spectrogram.WaveletSpectrogramVisualizerModel(**kwargs)[source]¶
Bases:
ViewModel
Traited class [tvb.adapters.visualizers.wavelet_spectrogram.WaveletSpectrogramVisualizerModel]¶
Attributes declared¶
- input_datatvb.adapters.visualizers.wavelet_spectrogram.WaveletSpectrogramVisualizerModel.input_data = DataTypeGidAttr(field_type=<class ‘uuid.UUID’>, default=None, required=True)
Wavelet spectrogram to display
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)
- input_data¶
Keep a GID but also link the type of DataType it should point to