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db Package

This is the module where all TVB Index DataTypes are hooked into the framework.

Define in __all__ attribute, modules to be introspected for finding their classes.

annotation

class tvb.adapters.datatypes.db.annotation.AnnotationTerm(id, parent, parent_left, parent_right, relation, label, definition=None, synonym=None, uri=None, tvb_left=None, tvb_right=None)[source]

Bases: builtins.object

One single annotation node (in the tree of annotations / region)

add_child(annotation_child)[source]
to_json(is_right_hemisphere=False, activation_patterns=None)[source]
to_tuple()[source]
class tvb.adapters.datatypes.db.annotation.ConnectivityAnnotationsIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

Ontology annotations for a Connectivity.

annotations_length
connectivity
connectivity_gid
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
parent_operation
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

connectivity

class tvb.adapters.datatypes.db.connectivity.ConnectivityIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

static accepted_filters()[source]
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
number_of_connections
number_of_regions
parent_operation
state
subject
title
tract_lengths_max
tract_lengths_mean
tract_lengths_min
type
type_
undirected
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
weights_max
weights_mean
weights_min

fcd

class tvb.adapters.datatypes.db.fcd.FcdIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataTypeMatrix

array_data_max
array_data_mean
array_data_min
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
labels_ordering
module
ndim
parent_operation
source
source_gid
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

graph

class tvb.adapters.datatypes.db.graph.ConnectivityMeasureIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataTypeMatrix

array_data_max
array_data_mean
array_data_min
connectivity
connectivity_gid
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
ndim
parent_operation
state
subject
subtype
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.graph.CorrelationCoefficientsIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataTypeMatrix

array_data_max
array_data_mean
array_data_min
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
labels_ordering
module
ndim
parent_operation
source
source_gid
state
subject
subtype
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.graph.CovarianceIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataTypeMatrix

array_data_max
array_data_mean
array_data_min
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
ndim
parent_operation
source
source_gid
state
subject
subtype
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

local_connectivity

class tvb.adapters.datatypes.db.local_connectivity.LocalConnectivityIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
matrix_non_zero_max
matrix_non_zero_mean
matrix_non_zero_min
module
parent_operation
state
subject
surface
surface_gid
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

mapped_value

class tvb.adapters.datatypes.db.mapped_value.DatatypeMeasureIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

Class to hold the metric for a previous stored DataType. E.g. Measure (single value) for any TimeSeries resulted in a group of Simulations

create_date
disk_size
display_name[source]

To be implemented in each sub-class which is about to be displayed in UI, and return the text to appear.

fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
metrics
module
parent_operation
source
source_gid
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.mapped_value.ValueWrapperIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

Class to wrap a singular value storage in DB.

create_date
data_name
data_type
data_value
disk_size
display_name[source]

Simple String to be used for display in UI.

fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
parent_operation
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

mode_decompositions

class tvb.adapters.datatypes.db.mode_decompositions.IndependentComponentsIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
parent_operation
source
source_gid
state
subject
subtype
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.mode_decompositions.PrincipalComponentsIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
parent_operation
source
source_gid
state
subject
subtype
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

patterns

class tvb.adapters.datatypes.db.patterns.StimuliRegionIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

connectivity
connectivity_gid
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
parent_operation
spatial_equation
spatial_parameters
state
subject
temporal_equation
temporal_parameters
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.patterns.StimuliSurfaceIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
parent_operation
spatial_equation
spatial_parameters
state
subject
surface
surface_gid
temporal_equation
temporal_parameters
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

projections

class tvb.adapters.datatypes.db.projections.ProjectionMatrixIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

brain_skull
brain_skull_gid
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
parent_operation
projection_type
sensors
sensors_gid
skin_air
skin_air_gid
skull_skin
skull_skin_gid
source
source_gid
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

region_mapping

class tvb.adapters.datatypes.db.region_mapping.RegionMappingIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

array_data_max
array_data_mean
array_data_min
connectivity
connectivity_gid
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
parent_operation
state
subject
surface
surface_gid
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.region_mapping.RegionVolumeMappingIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataTypeMatrix

array_data_max
array_data_mean
array_data_min
connectivity
connectivity_gid
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
ndim
parent_operation
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
volume
volume_gid

sensors

class tvb.adapters.datatypes.db.sensors.SensorsIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
number_of_sensors
parent_operation
sensors_type
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

simulation_state

class tvb.adapters.datatypes.db.simulation_state.SimulationStateIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

create_date
disk_size
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
parent_operation
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

spectral

class tvb.adapters.datatypes.db.spectral.CoherenceSpectrumIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataTypeMatrix

create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
frequencies_max
frequencies_min
gid
id
invalid
is_nan
module
ndim
nfft
parent_operation
source
source_gid
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.spectral.ComplexCoherenceSpectrumIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataTypeMatrix

create_date
disk_size
epoch_length
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
frequency_step
gid
id
invalid
is_nan
max_frequency
module
ndim
parent_operation
segment_length
source
source_gid
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
windowing_function
class tvb.adapters.datatypes.db.spectral.FourierSpectrumIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataTypeMatrix

create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
frequency_step
gid
id
invalid
is_nan
max_frequency
module
ndim
parent_operation
segment_length
source
source_gid
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
windowing_function
class tvb.adapters.datatypes.db.spectral.WaveletCoefficientsIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataTypeMatrix

create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
frequencies_max
frequencies_min
gid
id
invalid
is_nan
module
mother
ndim
normalisation
number_of_scales
parent_operation
q_ratio
sample_period
source
source_gid
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

structural

class tvb.adapters.datatypes.db.structural.StructuralMRIIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataTypeMatrix

array_data_max
array_data_mean
array_data_min
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
ndim
parent_operation
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
volume
volume_gid
weighting

surface

class tvb.adapters.datatypes.db.surface.SurfaceIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

bi_hemispheric
create_date
disk_size
edge_length_max
edge_length_mean
edge_length_min
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
number_of_edges
number_of_triangles
number_of_vertices
parent_operation
state
subject
surface_type
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
valid_for_simulations
visible

temporal_correlations

class tvb.adapters.datatypes.db.temporal_correlations.CrossCorrelationIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

array_data_max
array_data_mean
array_data_min
create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
labels_ordering
module
parent_operation
source
source_gid
state
subject
subtype
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

time_series

class tvb.adapters.datatypes.db.time_series.TimeSeriesEEGIndex(gid=None, **kwargs)[source]

Bases: tvb.adapters.datatypes.db.time_series.TimeSeriesIndex

create_date
data_length_1d
data_length_2d
data_length_3d
data_length_4d
data_ndim
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
has_surface_mapping
has_volume_mapping
id
invalid
is_nan
labels_dimensions
labels_ordering
module
parent_operation
sample_period
sample_period_unit
sample_rate
sensors
sensors_gid
start_time
state
subject
time_series_type
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.time_series.TimeSeriesIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

static accepted_filters()[source]
create_date
data_length_1d
data_length_2d
data_length_3d
data_length_4d
data_ndim
disk_size
fill_from_has_traits(datatype)[source]
fill_shape(final_shape)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
get_data_shape()[source]
get_labels_for_dimension(idx)[source]
gid
has_surface_mapping
has_volume_mapping
id
invalid
is_nan
labels_dimensions
labels_ordering
module
parent_operation
sample_period
sample_period_unit
sample_rate
start_time
state
subject
time_series_type
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.time_series.TimeSeriesMEGIndex(gid=None, **kwargs)[source]

Bases: tvb.adapters.datatypes.db.time_series.TimeSeriesIndex

create_date
data_length_1d
data_length_2d
data_length_3d
data_length_4d
data_ndim
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
has_surface_mapping
has_volume_mapping
id
invalid
is_nan
labels_dimensions
labels_ordering
module
parent_operation
sample_period
sample_period_unit
sample_rate
sensors
sensors_gid
start_time
state
subject
time_series_type
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.time_series.TimeSeriesRegionIndex(gid=None, **kwargs)[source]

Bases: tvb.adapters.datatypes.db.time_series.TimeSeriesIndex

connectivity
connectivity_gid
create_date
data_length_1d
data_length_2d
data_length_3d
data_length_4d
data_ndim
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
has_surface_mapping
has_volume_mapping
id
invalid
is_nan
labels_dimensions
labels_ordering
module
parent_operation
region_mapping
region_mapping_gid
region_mapping_volume
region_mapping_volume_gid
sample_period
sample_period_unit
sample_rate
start_time
state
subject
time_series_type
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.time_series.TimeSeriesSEEGIndex(gid=None, **kwargs)[source]

Bases: tvb.adapters.datatypes.db.time_series.TimeSeriesIndex

create_date
data_length_1d
data_length_2d
data_length_3d
data_length_4d
data_ndim
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
has_surface_mapping
has_volume_mapping
id
invalid
is_nan
labels_dimensions
labels_ordering
module
parent_operation
sample_period
sample_period_unit
sample_rate
sensors
sensors_gid
start_time
state
subject
time_series_type
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.time_series.TimeSeriesSurfaceIndex(gid=None, **kwargs)[source]

Bases: tvb.adapters.datatypes.db.time_series.TimeSeriesIndex

create_date
data_length_1d
data_length_2d
data_length_3d
data_length_4d
data_ndim
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
has_surface_mapping
has_volume_mapping
id
invalid
is_nan
labels_dimensions
labels_ordering
module
parent_operation
sample_period
sample_period_unit
sample_rate
start_time
state
subject
surface
surface_gid
time_series_type
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
class tvb.adapters.datatypes.db.time_series.TimeSeriesVolumeIndex(gid=None, **kwargs)[source]

Bases: tvb.adapters.datatypes.db.time_series.TimeSeriesIndex

create_date
data_length_1d
data_length_2d
data_length_3d
data_length_4d
data_ndim
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
has_surface_mapping
has_volume_mapping
id
invalid
is_nan
labels_dimensions
labels_ordering
module
parent_operation
sample_period
sample_period_unit
sample_rate
start_time
state
subject
time_series_type
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
volume
volume_gid

tracts

class tvb.adapters.datatypes.db.tracts.TractsIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
parent_operation
region_volume_map
region_volume_map_gid
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible

volume

class tvb.adapters.datatypes.db.volume.VolumeIndex(gid=None, **kwargs)[source]

Bases: tvb.core.entities.model.model_datatype.DataType

create_date
disk_size
fill_from_has_traits(datatype)[source]
fk_datatype_group
fk_from_operation
fk_parent_burst
gid
id
invalid
is_nan
module
parent_operation
state
subject
title
type
type_
user_tag_1
user_tag_2
user_tag_3
user_tag_4
user_tag_5
visible
voxel_unit