Biosignalsnotebooks

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Description

<span style="color:#009EE3">biosignalsnotebooks</span> is a set of documents and a <span style="color: #62C3EE">Python</span> library to provide programming examples in the form of <span style="color:#72BE94">Jupyter Notebooks</span>, as companion to the <span style="color:#009EE3">OpenSignals</span> biosignals acquisition tools.

This collection of code samples has the purpose to help users of PLUX Wireless Biosignals systems, such as BITalino or biosignalsplux, and to the researcher or student interested on recording processing and classifying biosignals. The examples are set on a level of complexity to inspire the users and programmers on how easy some tasks are and that more complex ones can also be achieved, by reusing and recreating some of the examples presented here.

A <span style="color: #62C3EE">Python</span> library (entitled <span style="color:#009EE3">biosignalsnotebooks</span> ) is the base toolbox to support the notebooks and to provide some useful functionalities. It can be installed through pip command, like demonstrated in a PyPI <img src="https://image.ibb.co/cNnx6V/link.png" width="10px" height="10px" style="display:inline"> dedicated page.

In many cases we also point and illustrate with code the usage of other python toolboxes dedicated to biosignal processing.

The notebooks will cover the full topics pipeline of working with biosignals, such as: <span style="color: #62C3EE">Load</span> a file; <span style="color:#AFE1F6">Visualise</span> the data online and offline, <span style="color:#00893E">Pre-Process</span> a one channel signal or a multi-channel acquisition, <span style="color:#72BE94">Detect</span> relevant events in the signals, <span style="#A8D7BD">Extract</span> features from many different type of sensors and domains, <span style="#CF0272">Train and Classify</span> among a set of classes with several machine learning approaches, <span style="#F0B2D4">Understand</span> the obtained results with metrics and validations techniques.

These examples are carried in a multitude of biosignals , from ECG, EDA, EMG, Accelerometer, Respiration among many others. The notebooks have a set of labels to help navigate among topics <a href="http://notebooks.pluxbiosignals.com/notebooks/Categories/MainFiles/by_tag_rev.html"><img src="https://image.ibb.co/cNnx6V/link.png" width="10px" height="10px" style="display:inline"></a>, types of signals <a href="http://notebooks.pluxbiosignals.com/notebooks/Categories/MainFiles/by_signal_type_rev.html"><img src="https://image.ibb.co/cNnx6V/link.png" width="10px" height="10px" style="display:inline"></a>, application area <a href="http://notebooks.pluxbiosignals.com/notebooks/Categories/MainFiles/biosignalsnotebooks_rev.html"><img src="https://image.ibb.co/cNnx6V/link.png" width="10px" height="10px" style="display:inline"></a> and complexity <a href="http://notebooks.pluxbiosignals.com/notebooks/Categories/MainFiles/by_diff_rev.html"><img src="https://image.ibb.co/cNnx6V/link.png" width="10px" height="10px" style="display:inline"></a> level to support the search for particular solutions.

We encourage you to share new example ideas, to pose questions helpdesk@pluxbiosignals.com, and to make improvements or suggestion to this set of notebooks.

Be inspired on how to make the most of your biosignals!

Available Notebooks

<table width="100%"> <tr> <td width="20%" align="center"><strong> Category <strong></td> <td width="80%"></td> </tr> <tr> <td rowspan='2'><p align='center'><img src='https://i.ibb.co/LgrhTz9/Install.png' width='50%' align='center'></p></td> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Install/prepare_anaconda_rev.html' target='_blank'> Download, Install and Execute Anaconda </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Install/prepare_jupyter_rev.html'> Download, Install and Execute Jupyter Notebook Environment </a> </td> </tr> <tr> <td rowspan='1'><p align='center'><img src='https://i.ibb.co/8cNpQFM/Connect.png' width='50%' align='center'></p></td> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Connect/pairing_device_rev.html' target='_blank'> Pairing a Device at Windows 10 [biosignalsplux] </a> </td> </tr> <tr> <td rowspan='5'><p align='center'><img src='https://i.ibb.co/d2jZH1s/Record.png' width='50%' align='center'></p></td> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Record/eeg_electrode_placement_rev.html' target='_blank'>EEG - Electrode Placement </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Record/record_data_rev.html'> Signal Acquisition [OpenSignals] </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Record/resolution_rev.html'> Resolution - The difference between smooth and abrupt variations </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Record/sampling_rate_and_aliasing_rev.html'>Problems of low sampling rate (aliasing)</a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Record/store_signals_after_acquisition_rev.html'> Store Files after Acquisition [OpenSignals] </a> </td> </tr> <tr> <td rowspan='5'><p align='center'><img src='https://i.ibb.co/YPbCnzD/Load.png' width='50%' align='center'></p></td> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Load/dataload_eeg_physionet_rev.html' target='_blank'> EEG - Loading Data from PhysioNet</a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Load/open_h5_rev.html'>Load acquired data from .h5 file</a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Load/open_signals_after_acquisition_rev.html'> Load Signals after Acquisition [OpenSignals] </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Load/open_txt_rev.html'>Load acquired data from .txt file</a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Load/signal_loading_preparatory_steps_rev.html'>Signal Loading - Working with File Header </a> </td> </tr> <tr> <td rowspan='1'><p align='center'><img src='https://i.ibb.co/wh4HKzf/Visualise.png' width='50%' align='center'></p></td> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Visualise/plot_acquired_data_single_rev.html' target='_blank'> Plotting of Acquired Data using Bokeh </a> </td> </tr> <tr> <td rowspan='25'><p align='center'><img src='https://i.ibb.co/1rKWccX/Pre-Process.png' width='50%' align='center'></p></td> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/digital_filtering_rev.html' target='_blank'> Digital Filtering - A Fundamental Pre-Processing Step </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/digital_filtering_eeg_rev.html'> Digital Filtering - EEG </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/digital_filtering_filtfilt_rev.html'> Digital Filtering - Using filtfilt </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/emg_fatigue_evaluation_median_freq_rev.html'>Fatigue Evaluation - Evolution of Median Power Frequency</a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/generation_of_time_axis_rev.html'> Generation of a time axis (conversion of samples into seconds) </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/poincare_plot_rev.html'> Generation of Poincar&eacute; Plot from ECG Analysis</a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/snr_determination_rev.html'> Signal to Noise Ratio Determination </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/snr_ECG_rev.html'> Computing SNR for ECG Signals </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/snr_slow_signals_rev.html'> Computing SNR for Slow Signals </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/synchronisation_rev.html'> Device Synchronisation - Cable, Light and Sound Approaches </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/synchrony_acc_rev.html'> Synchrony - Accelerometer Signal </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/synchrony_light_rev.html'> Synchrony - Light Signal </a> </td> </tr> <tr> <td align='center'> <a href='http://notebooks.pluxbiosignals.com/notebooks/Categories/Pre-Process/synchrony_sound_rev.html'> S