BrainSense Streaming Pipeline

Overview

The BrainSense Streaming Pipeline is a Python module specific for handling BrainSense Streaming data format from Percept. This section will go over all functions implemented and provide sufficient details on pipeline implementation.

Methods

Percept.BrainSenseStream.saveRealtimeStreams(deviceID, StreamingTD, StreamingPower, sourceFile)

Save BrainSense Streaming Data in Database Storage

Parameters

  • deviceID – UUID4 deidentified id for each unique Percept device.

  • StreamingTD – BrainSense TimeDomain structure extracted from Medtronic JSON file.

  • StreamingPower – BrainSense Power Channel structure extracted from Medtronic JSON file.

  • sourceFile – filename of the raw JSON file that the original data extracted from.

Returns

Boolean indicating if new data is found (to be saved).

Percept.BrainSenseStream.processRealtimeStreams(stream, cardiacFilter=False)

Process BrainSense Streaming Data

This is the primary processing function for all BrainSense Streaming data. The server will attempt to calculate Short-time Fourier Transform (STFT) with 1.0 second window and 0.5 second overlap. In addition to the STFT, the server will also calculate Wavelet Transform with a 500ms moving average window.

The user can request the server to perform cardiac removal using cardiacFilter argument. If cardiac filter is used, the server will perform a template matching algorithm to remove cardiac signals. (TODO: details algorithm for later).

Parameters

  • stream – BrainSense TimeDomain structure extracted from Medtronic JSON file

  • cardiacFilter – Boolean indicating if you want to .

Returns

Processed BrainSense TimeDomain structure

Percept.BrainSenseStream.queryRealtimeStreamRecording(analysis, cardiacFilter=False, refresh=False)

Query BrainSense Streaming Data

This function will query BrainSense recording data based on provided Recording ID.

Parameters

  • user – BRAVO Platform User object.

  • recordingId – Deidentified recording ID as referenced in SQL Database.

  • authority – User permission structure indicating the type of access the user has.

  • cardiacFilter – Boolean indicator if the user want to apply cardiac filters (see processRealtimeStreams function)

  • refresh – Boolean indicator if the user want to use cache data or reprocess the data.

Returns

Returns a tuple (BrainSenseData, RecordingID) where BrainSenseData is the BrainSense streaming data structure in Database and RecordingID is the deidentified id of the available data.

Percept.BrainSenseStream.queryMultipleSegmentComparison(user, recordingIds, authority)

Query Multiple Segment Comparison

This function will query BrainSense recording data based on provided Recording ID.

Parameters

  • user – BRAVO Platform User object.

  • recordingIds – List of deidentified recording IDs as referenced in SQL Database.

  • authority – User permission structure indicating the type of access the user has.

Returns

Returns a dictionary (SegmentSummaries) which contains average power spectrum and respective stimulation settings.

Percept.BrainSenseStream.processRealtimeStreamRenderingData(stream, options={}, centerFrequencies=[0, 0], stimulationReference='Ipsilateral')

Process BrainSense Streaming Data to be used for Plotly rendering.

This function takes the processRealtimeStreams BrainSense Stream object and further process it for frontend rendering system. This is to reduce some computational requirement for the frontend, and because Python signal processing is more efficient than Javascript frontend.

This function wrap around processRealtimeStreamStimulationPSD function to generate stimulation related PSD at different stimulation state.

Parameters

  • stream – processed BrainSense TimeDomain structure (see processRealtimeStreams function)

  • options – Signal processing module configurations.

  • centerFrequencies – The center frequencies (Left and Right hemisphere) used to obtain Power-band box plot.

Returns

Returns processed data object with content sufficient for React.js to render Plotly graphs.

Percept.BrainSenseStream.processRealtimeStreamStimulationAmplitude(stream)

Process BrainSense Streaming Data to extract data segment at different stimulation amplitude.

Parameters

stream – processed BrainSense PowerDomain structure (see processRealtimeStreams function)

Returns

Returns list of stimulation series.

Percept.BrainSenseStream.processRealtimeStreamPowerBand(stream)

Extract Onboard Power-band recording.

Additional filtering is done by performing zscore normalization. Outliers are removed.

Parameters

stream – processed BrainSense PowerDomain structure (see processRealtimeStreams function)

Returns

Returns list of stimulation series.

Percept.BrainSenseStream.processRealtimeStreamStimulationPSD(stream, channel, method='Spectrogram', stim_label='Ipsilateral', centerFrequency=0)

Process BrainSense Stream Stimulation-specific Power Spectrum

The process will take in stimulation epochs and compute Power Spectral Density using methods specified in parameters. Stimulation epochs with less than 7 seconds of recording are skipped. 2 seconds before and after stimulation changes are skipped to avoid transition artifacts.

Standard method uses 1 second Window and 0.5 seconds overlap. Standard Spectral Feature bandwidth is +/- 2Hz.

Parameters

  • stream – processed BrainSense TimeDomain structure (see processRealtimeStreams function)

  • channel – BrainSense TimeDomain data channel name.

  • method (string) – Processing method. Default to “Spectrogram” method, can be one of (Welch, Spectrogram, or Wavelet).

  • stim_label (string) – Using “Ipsilateral” stimulation label or “Contralateral” stimulation label.

  • centerFrequency (int) – The center frequency at which the spectral features are extracted from PSD.

Returns

Returns average PSD at each stimulation amplitude, and Spectral Features extracted from desired frequency band.