creators Package

# analyzers Package¶

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

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

Interface between Brain Connectivity Toolbox of Olaf Sporns and TVB Framework. This adapter requires BCT deployed locally, and Matlab or Octave installed separately of TVB.

build_connectivity_measure(result, key, connectivity, title='', label_x='', label_y='')[source]
build_float_value_wrapper(result, key, title='')[source]
build_int_value_wrapper(result, key, title='')[source]
static can_be_active()[source]
execute_matlab(matlab_code, **kwargs)[source]
get_form_class()[source]
get_output()[source]
get_required_disk_size(**kwargs)[source]
get_required_memory_size(**kwargs)[source]
launch(connectivity, **kwargs)[source]
static get_connectivity_label()[source]
static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]
get_form_class()[source]
launch(connectivity, **kwargs)[source]
static get_connectivity_label()[source]
static get_filters()[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]

launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]

launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]

launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]
launch(connectivity, **kwargs)[source]

Adapter that uses the traits module to generate interfaces for ... Analyzer.

Model class defining the traited attributes used by the CorrelationCoefficientAdapter.
time_series : tvb.adapters.analyzers.cross_correlation_adapter.CorrelationCoefficient.time_series = Attr(field_type=<class ‘tvb.datatypes.time_series.TimeSeries’>, default=None, required=True)
The time-series for which the cross correlation matrices are calculated.
t_start : tvb.adapters.analyzers.cross_correlation_adapter.CorrelationCoefficient.t_start = Float(field_type=<class ‘float’>, default=0.9765625, required=True)
Time start point (ms). By default it uses the default Monitor sample period. The starting time point of a time series is not zero, but the monitor’s sample period.
t_end : tvb.adapters.analyzers.cross_correlation_adapter.CorrelationCoefficient.t_end = Float(field_type=<class ‘float’>, default=1000.0, required=True)
End time point (ms)

gid : tvb.basic.neotraits._core.HasTraits.gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=True)

t_end

Declares a float. This is different from Attr(field_type=float). The former enforces float subtypes. This allows any type that can be safely cast to the declared float type according to numpy rules.

Reading and writing this attribute is slower than a plain python attribute. In performance sensitive code you might want to use plain python attributes or even better local variables.

t_start

Declares a float. This is different from Attr(field_type=float). The former enforces float subtypes. This allows any type that can be safely cast to the declared float type according to numpy rules.

Reading and writing this attribute is slower than a plain python attribute. In performance sensitive code you might want to use plain python attributes or even better local variables.

time_series

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.

Model class defining the traited attributes used by the CrossCorrelateAdapter.
time_series : tvb.adapters.analyzers.cross_correlation_adapter.CrossCorrelate.time_series = Attr(field_type=<class ‘tvb.datatypes.time_series.TimeSeries’>, default=None, required=True)
The time-series for which the cross correlation sequences are calculated.

gid : tvb.basic.neotraits._core.HasTraits.gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=True)

time_series

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.

TVB adapter for calling the CrossCorrelate algorithm.

configure(time_series)[source]

Store the input shape to be later used to estimate memory usage.

Parameters: time_series – the input time-series index for which cross correlation should be computed
get_form_class()[source]
get_output()[source]
get_required_disk_size(**kwargs)[source]

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

get_required_memory_size(**kwargs)[source]

Returns the required memory to be able to run the adapter.

launch(time_series)[source]

Launch algorithm and build results. Compute the node-pairwise cross-correlation of the source 4D TimeSeries represented by the index given as input.

Return a CrossCorrelationIndex. Create a CrossCorrelationH5 that contains the cross-correlation sequences for all possible combinations of the nodes.

Parameters: time_series – the input time series index for which the correlation should be computed the cross correlation index for the given time series CrossCorrelationIndex
static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]

TVB adapter for calling the Pearson correlation coefficients algorithm.

configure(time_series, t_start, t_end)[source]

Store the input shape to be later used to estimate memory usage.

Parameters: time_series – the input time-series index for which correlation coefficient should be computed t_start – the physical time interval start for the analysis t_end – physical time, interval end
get_form_class()[source]
get_output()[source]
get_required_disk_size(**kwargs)[source]

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

get_required_memory_size(**kwargs)[source]

Returns the required memory to be able to run this adapter.

launch(time_series, t_start, t_end)[source]

Launch algorithm and build results. Compute the node-pairwise pearson correlation coefficient of the given input 4D TimeSeries datatype.

The result will contain values between -1 and 1, inclusive.

Parameters: time_series – the input time-series for which correlation coefficient should be computed t_start – the physical time interval start for the analysis t_end – physical time, interval end the correlation coefficient for the given time series CorrelationCoefficients
static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]
get_traited_datatype()[source]

Adapter that uses the traits model to generate interfaces for FCD Analyzer.

static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]
get_traited_datatype()[source]
Model class defining the traited attributes used by the FcdAdapter.
time_series : tvb.adapters.analyzers.fcd_adapter.FcdCalculator.time_series = Attr(field_type=<class ‘tvb.datatypes.time_series.TimeSeriesRegion’>, default=None, required=True)
The time-series for which the fcd matrices are calculated.
sw : tvb.adapters.analyzers.fcd_adapter.FcdCalculator.sw = Float(field_type=<class ‘float’>, default=120000, required=True)
Length of the time window used to divided the time series. FCD matrix is calculated in the following way: the time series is divided in time window of fixed length and with an overlapping of fixed length. The data-points within each window, centered at time ti, are used to calculate FC(ti) as Pearson correlation. The ij element of the FCD matrix is calculated as the Pearson Correlation between FC(ti) and FC(tj) arranged in a vector.
sp : tvb.adapters.analyzers.fcd_adapter.FcdCalculator.sp = Float(field_type=<class ‘float’>, default=2000, required=True)
Spanning= (time windows length)-(overlapping between two consecutive time window). FCD matrix is calculated in the following way: the time series is divided in time window of fixed length and with an overlapping of fixed length. The data-points within each window, centered at time ti, are used to calculate FC(ti) as Pearson Correlation. The ij element of the FCD matrix is calculated as the Pearson correlation between FC(ti) and FC(tj) arranged in a vector

gid : tvb.basic.neotraits._core.HasTraits.gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=True)

sp

Declares a float. This is different from Attr(field_type=float). The former enforces float subtypes. This allows any type that can be safely cast to the declared float type according to numpy rules.

Reading and writing this attribute is slower than a plain python attribute. In performance sensitive code you might want to use plain python attributes or even better local variables.

sw

Declares a float. This is different from Attr(field_type=float). The former enforces float subtypes. This allows any type that can be safely cast to the declared float type according to numpy rules.

Reading and writing this attribute is slower than a plain python attribute. In performance sensitive code you might want to use plain python attributes or even better local variables.

time_series

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.

TVB adapter for calling the Pearson CrossCorrelation algorithm.

The present class will do the following actions:

• Compute the the fcd of the timeseries; the fcd is calculated in the following way:

the time series is divided in time window of fixed length and with an overlapping of fixed length. The data-points within each window, centered at time ti, are used to calculate FC(ti) as Pearson correlation The ij element of the FCD matrix is calculated as the Pearson correlation between FC(ti) and FC(tj) -in a vector

• Apply to the fcd the spectral embedding algorithm in order to calculate epochs of stability of the fcd

(length of time during which FC matrix are high correlated).

The algorithm can produce 2 kind of results:

• case 1: the algorithm is able to identify the epochs of stability

– fcs calculated over the epochs of stability (excluded the first one = artifact, due to initial conditions) – 3 eigenvectors, associated to the 3 largest eigenvalues, of the fcs are extracted

• case 2: the algorithm is not able to identify the epochs of stability

– fc over the all time series is calculated – 3 first eigenvectors, associated to the 3 largest eigenvalues, of the fcs are extracted

:return
• fcd matrix whose values are between -1 and 1, inclusive.

• in case 1: fcd matrix segmented i.e. fcd whose values are between -1 and 1.1, inclusive.

(Value=1.1 for time not belonging to epochs of stability identified with spectral embedding algorithm) in case 2: fcd matrix segmented identical to the fcd matrix not segmented

• dictionary containing the eigenvectors.

• dictionary containing the eigenvalues

• connectivity associated to the TimeSeriesRegions

configure(time_series, sw, sp)[source]

Store the input shape to be later used to estimate memory usage. Also create the algorithm instance.

Parameters: time_series – the input time-series for which fcd matrix should be computed sw – length of the sliding window sp – spanning time: distance between two consecutive sliding window
get_form_class()[source]
get_output()[source]
get_required_disk_size(**kwargs)[source]
get_required_memory_size(**kwargs)[source]
launch(time_series, sw, sp)[source]

Launch algorithm and build results.

Parameters: time_series – the input time-series index for which fcd matrix should be computed sw – length of the sliding window sp – spanning time: distance between two consecutive sliding window the fcd index for the computed fcd matrix on the given time-series, with that sw and that sp FcdIndex,ConnectivityMeasureIndex

Adapter that uses the traits module to generate interfaces for BalloonModel Analyzer.

TVB adapter for calling the BalloonModel algorithm.

configure(time_series, dt=None, bold_model=None, RBM=None, neural_input_transformation=None)[source]

Store the input shape to be later used to estimate memory usage. Also create the algorithm instance.

get_form_class()[source]
get_output()[source]
get_required_disk_size(**kwargs)[source]

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

get_required_memory_size(**kwargs)[source]

Return the required memory to run this algorithm.

launch(time_series, dt=None, bold_model=None, RBM=None, neural_input_transformation=None)[source]

Launch algorithm and build results.

Parameters: time_series – the input time-series used as neural activation in the Balloon Model the simulated BOLD signal TimeSeries
static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]
get_traited_datatype()[source]

Adapter that uses the traits module to generate interfaces for FFT Analyzer.

static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]
get_traited_datatype()[source]

TVB adapter for calling the FFT algorithm.

configure(time_series, segment_length=None, window_function=None, detrend=None)[source]

Do any configuration needed before launching.

Parameters: time_series – the input time series to which the fft is to be applied segment_length – the block size which determines the frequency resolution of the resulting power spectra window_function (None; ‘hamming’; ‘bartlett’; ‘blackman’; ‘hanning’) – windowing functions can be applied before the FFT is performed detrend – None; specify if detrend is performed on the time series
get_form_class()[source]
get_output()[source]
get_required_disk_size(time_series, segment_length=None, window_function=None, detrend=None)[source]

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

get_required_memory_size(time_series, segment_length=None, window_function=None, detrend=None)[source]

Returns the required memory to be able to run the adapter.

launch(time_series, segment_length=None, window_function=None, detrend=None)[source]

Launch algorithm and build results.

Parameters: time_series – the input time series to which the fft is to be applied segment_length – the block size which determines the frequency resolution of the resulting power spectra window_function (None; ‘hamming’; ‘bartlett’; ‘blackman’; ‘hanning’) – windowing functions can be applied before the FFT is performed the fourier spectrum for the specified time series FourierSpectrumIndex

Adapter that uses the traits module to generate interfaces for ICA Analyzer.

TVB adapter for calling the ICA algorithm.

configure(time_series, n_components=None)[source]

Store the input shape to be later used to estimate memory usage. Also create the algorithm instance.

get_form_class()[source]
get_output()[source]
get_required_disk_size(time_series, n_components=None)[source]

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

get_required_memory_size(time_series, n_components=None)[source]

Return the required memory to run this algorithm.

launch(time_series, n_components=None)[source]

Launch algorithm and build results.

static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]
get_traited_datatype()[source]

## matlab_worker¶

This module implements a class for executing arbitray MATLAB code

Conversion between Python types and MATLAB types is handled and dependent on scipy.io’s loadmat and savemat function.

Bases: builtins.object

MatlabAnalyzer is an helper class for calling arbitrary MATLAB code with arbitrary parameters.

Specific analyzers should derive from this class and implement the interface and launch methods inherited from Asynchronous Adapter.

Add a path to the list of paths that will be added to the path in the MATLAB session

cleanup()[source]

Make sure Matlab is closed after execution.

matlab(code, data=None, work_dir=None, cleanup=True)[source]

method matlab takes as arguments:

code: MATLAB code in a string data: a dict of data that scipy.io.savemat knows how to deal with work_dir: working directory to be used by MATLAB cleanup: set to False to keep files

and returns a tuple:

[0] string of code exec’d by MATLAB [1] string of log produced by MATLAB [2] dict of data from MATLAB’s workspace
matlab_paths = []

## metrics_group_timeseries¶

Adapter that uses the traits module to generate interfaces for group of Analyzer used to calculate a single measure for TimeSeries.

TVB adapter for exposing as a group the measure algorithm.

configure(time_series, **kwargs)[source]

Store the input shape to be later used to estimate memory usage.

get_form_class()[source]
get_output()[source]
get_required_disk_size(**kwargs)[source]

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

get_required_memory_size(**kwargs)[source]

Return the required memory to run this algorithm.

input_shape = ()
launch(time_series, algorithms=None, start_point=None, segment=None)[source]

Launch algorithm and build results.

Parameters: time_series – the time series on which the algorithms are run algorithms (any subclass of BaseTimeseriesMetricAlgorithm (KuramotoIndex, GlobalVariance, VarianceNodeVariance)) – the algorithms to be run for computing measures on the time series DatatypeMeasureIndex
static get_extra_algorithm_filters()[source]
static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]

Adapter that uses the traits module to generate interfaces for FFT Analyzer.

TVB adapter for calling the NodeCoherence algorithm.

configure(time_series, nfft=None)[source]

Store the input shape to be later used to estimate memory usage. Also create the algorithm instance.

get_form_class()[source]
get_output()[source]
get_required_disk_size(**kwargs)[source]

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

get_required_memory_size(**kwargs)[source]

Return the required memory to run this algorithm.

launch(time_series, nfft=None)[source]

Launch algorithm and build results.

static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]
get_traited_datatype()[source]

Adapter that uses the traits module to generate interfaces for FFT Analyzer.

TVB adapter for calling the NodeComplexCoherence algorithm.

configure(time_series)[source]

Do any configuration needed before launching and create an instance of the algorithm.

get_form_class()[source]
get_output()[source]
get_required_disk_size(**kwargs)[source]

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

get_required_memory_size(**kwargs)[source]

Return the required memory to run this algorithm.

launch(time_series)[source]

Launch algorithm and build results.

Returns: the ComplexCoherenceSpectrum built with the given time-series
static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]
get_traited_datatype()[source]

Adapter that uses the traits module to generate interfaces for FFT Analyzer.

Model class defining the traited attributes used by the NodeCovarianceAdapter.
time_series : tvb.adapters.analyzers.node_covariance_adapter.NodeCovariance.time_series = Attr(field_type=<class ‘tvb.datatypes.time_series.TimeSeries’>, default=None, required=True)
The timeseries to which the NodeCovariance is to be applied.

gid : tvb.basic.neotraits._core.HasTraits.gid = Attr(field_type=<class ‘uuid.UUID’>, default=None, required=True)

time_series

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.

TVB adapter for calling the NodeCovariance algorithm.

configure(time_series)[source]

Store the input shape to be later used to estimate memory usage.

get_form_class()[source]
get_output()[source]
get_required_disk_size(**kwargs)[source]

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

get_required_memory_size(**kwargs)[source]

Return the required memory to run this algorithm.

launch(time_series)[source]

Launch algorithm and build results.

Returns: the CovarianceIndex built with the given time_series index as source
static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]

Adapter that uses the traits module to generate interfaces for FFT Analyzer.

TVB adapter for calling the PCA algorithm.

configure(time_series)[source]

Store the input shape to be later used to estimate memory usage. Also create the algorithm instance.

get_form_class()[source]
get_output()[source]
get_required_disk_size(time_series)[source]

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

get_required_memory_size(time_series)[source]

Return the required memory to run this algorithm.

launch(time_series)[source]

Launch algorithm and build results.

Returns: the PrincipalComponents object built with the given timeseries as source
static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]
get_traited_datatype()[source]

Adapter that uses the traits module to generate interfaces for ContinuousWaveletTransform Analyzer.

TVB adapter for calling the ContinuousWaveletTransform algorithm.

configure(time_series, mother=None, sample_period=None, normalisation=None, q_ratio=None, frequencies='Range', frequencies_parameters=None)[source]

Store the input shape to be later used to estimate memory usage. Also create the algorithm instance.

get_form_class()[source]
get_output()[source]
get_required_disk_size(**kwargs)[source]

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

get_required_memory_size(**kwargs)[source]

Return the required memory to run this algorithm.

launch(time_series, mother=None, sample_period=None, normalisation=None, q_ratio=None, frequencies='Range', frequencies_parameters=None)[source]

Launch algorithm and build results.