cognify 0.0.7

DataScience environment for Insai BCI

Cognify - Insai Cognition Lab

Getting Started

To get started, you just need install the cognify library. The libary is constantly evolving so stay tuned for new updates.

Install

Begin by installing the cognify library, by running in your terminal

pip install cognify

Next, you need to add a separate config file containing the database credentials. This file is provided upon request. It will need to be added to the folder where cognify was installed.

To find the installation location simply run

pip show cognify

This should give you the location of the cognify library

Navigate to that the cognify folder and place the settings.ini file that will be provided inside the folder.

Import libraries

Data Retrieval

It is important after recording your biometric data to have access to the raw data. This section shows how to extract the raw data from your device depending on the biosignal (EEG, PPG, Acelerometer or Gyroscope).

All recorded data is stored securely in a database.

We have created simple functions to retrieve the raw data based on your User ID. Therefore, only you have access to your data.

You will obtain your User ID after creating your profile on the Insai platform (https://insai.app/signup)

EEG

To begin, you can view all the recordings from a specific user, based on their User ID.

As you can observe, the creation data and type of recording are displayed to identify the recording you want to analyze.

After identifying the recording you want to analyze, note down the Metric ID, this is unique to each recording and serves as an identifier to get access to all biometric data linked to that recording.

In this example, my User ID is ck9jusufs000016pbioyzehto

And the recording I will analyse will be a reading session recorded at 6:35am, 2021-03-09. The metric ID is ckm1n2i2y24577515snzllm3jxe

userId='ck9jusufs000016pbioyzehto'
recordings = dataset.get_recordings(userId)
recordings.tail()

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	metricId	type	userId	createdAt	startTime	stopTime
142	cklujacpy119754916nk1jpgwsxp	Reading	ck9jusufs000016pbioyzehto	2021-03-04 07:14:52.006	"2021-03-04T07:14:51.837Z"	2021-03-04T07:52:18.146Z
143	cklvxp8nw150056716nk44eebuep	Reading	ck9jusufs000016pbioyzehto	2021-03-05 06:46:07.389	"2021-03-05T06:46:07.128Z"	2021-03-05T07:04:40.952Z
144	cklvyhjl8120897116nkythrdgkl	Reading	ck9jusufs000016pbioyzehto	2021-03-05 07:08:07.916	"2021-03-05T07:08:07.720Z"	2021-03-05T08:12:21.094Z
145	ckm1n2i2y24577515snzllm3jxe	Reading	ck9jusufs000016pbioyzehto	2021-03-09 06:35:07.402	"2021-03-09T06:35:07.234Z"	2021-03-09T06:48:31.988Z
146	ckm32gn98122155015snwkcr5u8y	Reading	ck9jusufs000016pbioyzehto	2021-03-10 06:33:47.708	"2021-03-10T06:33:47.401Z"	2021-03-10T07:00:59.551Z

Dataframe

After identifying the recording I want to analyze and the associated Metric ID ckm1n2i2y24577515snzllm3jxe. I can now begin retrieving the raw EEG data from the database.

The EEG data is retrieved and converted into a Pandas Dataframe.

In this format, each column represents the electrical activity from a given electrode and the timestamp is provided as the index.

There is additional information regarding how the data was sent from the device to the computer (using buffers).

metricId = 'ckm1n2i2y24577515snzllm3jxe'
eeg = dataset.get_eeg(metricId)
df_eeg = dataset.eeg_to_df(eeg)
df_eeg.head()

Each buffer is 3 seconds long
Each buffer is sampled every 1.5 seconds
The number of buffers skipped 0
Number of timestamps:  337920
Number of unique timestamps:  337920
Some timestamps had different data values, this affected approximately 0.00 % of the data

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	TP9	AF7	AF8	TP10
time
2021-03-09 06:35:05.812125000	-1000.000000000000000000000000000000	-1000.000000000000000000000000000000	-662.109375000000000000000000000000	-1000.000000000000000000000000000000
2021-03-09 06:35:05.816031250	-1000.000000000000000000000000000000	-431.152343750000000000000000000000	-374.023437500000000000000000000000	-859.863281250000000000000000000000
2021-03-09 06:35:05.819937500	172.851562500000000000000000000000	275.390625000000000000000000000000	24.902343750000000000000000000000	64.453125000000000000000000000000
2021-03-09 06:35:05.823843750	-962.402343750000000000000000000000	436.523437500000000000000000000000	223.144531250000000000000000000000	684.570312500000000000000000000000
2021-03-09 06:35:05.827750000	-388.671875000000000000000000000000	-265.136718750000000000000000000000	-81.054687500000000000000000000000	-181.152343750000000000000000000000

MNE

Alternatively, the data can directly be exported to MNE.

By default, a bandpass filtered [1, 40] Hz is applied by default, but this can be removed.

It returns:

• Raw data in MNE format
• Events related to the task (if a task was undertaken on the Insai Platform: N-back, Digit Span or Sternberg)
• Raw data in a dataframe

metricId = 'ckkymq9fx5695271gntqvd743uk'
raw,events,df_eeg = dataset.eeg_to_mne(metricId)

Each buffer is 3 seconds long
Each buffer is sampled every 1.5 seconds
The number of buffers skipped 0
Number of timestamps:  82944
Number of unique timestamps:  82944
Some timestamps had different data values, this affected approximately 0.00 % of the data
Creating RawArray with float64 data, n_channels=4, n_times=41856
    Range : 0 ... 41855 =      0.000 ...   163.496 secs
Ready.

Display the data information

raw.info

<Info | 8 non-empty values
 bads: []
 ch_names: TP9, AF7, AF8, TP10
 chs: 4 EEG
 custom_ref_applied: False
 dig: 7 items (3 Cardinal, 4 EEG)
 highpass: 1.0 Hz
 lowpass: 40.0 Hz
 meas_date: unspecified
 nchan: 4
 projs: []
 sfreq: 256.0 Hz
>

PPG

The Metric ID cklv4n4gk9375316nk687ui65p can be used to retrieve the PPG data from a specific recording, you can retrieve the PPG data from the database.

PPG can be used to retrieve the heart rate and more in-depth heart-related metrics, such as pulse rate variability (PRV), which has shown some correlations with Heart Rate Variability (HRV).

Dataframe

The PPG data is retrieved and converted into three Pandas Dataframes.

Each dataframe contains the signal and timestamps for a given sensor channel.

There are three channels Ambient, Infrared and Red.

With some simple preprocessing, the heart rate can be retrieved from the Infrared signal.

metricId = 'cklv4n4gk9375316nk687ui65p'
ppg = dataset.get_ppg(metricId)
df_ppg = dataset.ppg_to_df(ppg)

Ambient

df_ppg[0]

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	Ambient
timestamp
2021-03-04 17:12:31.211250	31455.000000000000000000000000000000
2021-03-04 17:12:31.226875	31449.000000000000000000000000000000
2021-03-04 17:12:31.242500	31395.000000000000000000000000000000
2021-03-04 17:12:31.258125	31488.000000000000000000000000000000
2021-03-04 17:12:31.273750	31532.000000000000000000000000000000
...	...
2021-03-04 17:21:08.351875	33073.000000000000000000000000000000
2021-03-04 17:21:08.367500	33066.000000000000000000000000000000
2021-03-04 17:21:08.383125	33069.000000000000000000000000000000
2021-03-04 17:21:08.398750	33080.000000000000000000000000000000
2021-03-04 17:21:08.414375	33117.000000000000000000000000000000

33102 rows × 1 columns

Infrared

df_ppg[1]

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	Infrared
timestamp
2021-03-04 17:12:31.211250	238546.000000000000000000000000000000
2021-03-04 17:12:31.226875	238704.000000000000000000000000000000
2021-03-04 17:12:31.242500	238496.000000000000000000000000000000
2021-03-04 17:12:31.258125	238286.000000000000000000000000000000
2021-03-04 17:12:31.273750	237916.000000000000000000000000000000
...	...
2021-03-04 17:21:08.351875	248397.000000000000000000000000000000
2021-03-04 17:21:08.367500	248360.000000000000000000000000000000
2021-03-04 17:21:08.383125	248397.000000000000000000000000000000
2021-03-04 17:21:08.398750	248290.000000000000000000000000000000
2021-03-04 17:21:08.414375	248326.000000000000000000000000000000

33102 rows × 1 columns

Red

df_ppg[2]

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	Red
timestamp
2021-03-04 17:12:31.211250	25.000000000000000000000000000000
2021-03-04 17:12:31.226875	0E-30
2021-03-04 17:12:31.242500	0E-30
2021-03-04 17:12:31.258125	0E-30
2021-03-04 17:12:31.273750	0E-30
...	...
2021-03-04 17:21:08.351875	36.000000000000000000000000000000
2021-03-04 17:21:08.367500	0E-30
2021-03-04 17:21:08.383125	0E-30
2021-03-04 17:21:08.398750	0E-30
2021-03-04 17:21:08.414375	0E-30

33102 rows × 1 columns

begin, end  = 1500,2500
plt.subplot(311)
plt.plot(df_ppg[0].to_numpy()[begin:end])
plt.ylabel('Ambient')
plt.subplot(312)
plt.plot(df_ppg[1].to_numpy()[begin:end])
plt.ylabel('IR')
plt.subplot(313)
plt.plot(df_ppg[2].to_numpy()[begin:end])
plt.ylabel('Red')
plt.xlabel("seconds")

Text(0.5, 0, 'seconds')



11-Mar-21 12:24:35 | WARNING | findfont: Font family ['normal'] not found. Falling back to DejaVu Sans.

Heart rate (In development)

The heart rate can be calculated from the PPG signal.

Simple preprocessing can done to clean up the signal and extract the heart rate.

The segment width (in seconds) and segment overlap (in seconds) can be configured to obtain the heart rate.

metricId = 'cklvxp8nw150056716nk44eebuep'
df_hr = heartrate.get_hr(metricId,segment_width=30, segment_overlap = 0.9)

G:\Programs\anaconda3\lib\site-packages\scipy\interpolate\fitpack2.py:253: UserWarning: 
The maximal number of iterations maxit (set to 20 by the program)
allowed for finding a smoothing spline with fp=s has been reached: s
too small.
There is an approximation returned but the corresponding weighted sum
of squared residuals does not satisfy the condition abs(fp-s)/s < tol.
  warnings.warn(message)

df_hr.head()

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	timestamp	hr
0	0.0	95.929464
1	3.0	96.145675
2	6.0	93.090909
3	9.0	91.569231
4	12.0	91.366417

plt.plot(df_hr['hr'])
plt.title('Heart rate over time')
plt.xlabel('Time (s)')
plt.ylabel('Heart rate (bpm)')

Text(0, 0.5, 'Heart rate (bpm)')

Accelerometer and Gyroscope

The Metric ID ckjsogpjw2206420ypu7iuepcth can be used to retrieve the Accelerometer (Accel) and Gyroscope (Gyro) data from a specific recording, you can retrieve the Accel and Gyro data from the database.

Accelerometer and Gyroscope may be useful to use to detect motion artifact and denoise other biosignals.

Dataframe

The Accel and Gyro data is retrieved and converted into Dataframes.

Each dataframe contains the signal along the X,Y and Z axis and the associated timestamps.

metricId = 'ckjsogpjw2206420ypu7iuepcth'
accel = dataset.get_xyz(metricId,'Accelerometer')
gyro = dataset.get_xyz(metricId,'Gyroscope')
df_accel = dataset.motion_to_df(accel)
df_gyro = dataset.motion_to_df(gyro)

df_accel.head()

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	x	y	z	timestamp
time
2021-01-11 14:44:53.210049072	0.187011852800000000000000000000	0.076599176000000000000000000000	0.994751689600000000000000000000	1610376293210.049000000000000000000000000000
2021-01-11 14:44:53.229279841	0.182190072000000000000000000000	0.078308161600000000000000000000	0.994507548800000000000000000000	1610376293210.049000000000000000000000000000
2021-01-11 14:44:53.248510610	0.179138312000000000000000000000	0.079101619200000000000000000000	0.994629619200000000000000000000	1610376293210.049000000000000000000000000000
2021-01-11 14:44:53.267740967	0.178039678400000000000000000000	0.078064020800000010000000000000	0.988281958400000000000000000000	1610376293267.741000000000000000000000000000
2021-01-11 14:44:53.286971736	0.178100713600000000000000000000	0.069946339200000000000000000000	0.996521710400000000000000000000	1610376293267.741000000000000000000000000000

df_gyro.head()

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	x	y	z	timestamp
time
2021-01-11 14:44:53.209049072	0.216827200000000000000000000000	-3.080441600000000000000000000000	1.061705600000000000000000000000	1610376293209.049000000000000000000000000000
2021-01-11 14:44:53.228279841	0.007476800000000000000000000000	-3.409420800000000000000000000000	0.852355200000000000000000000000	1610376293209.049000000000000000000000000000
2021-01-11 14:44:53.247510610	-0.022430400000000000000000000000	-3.229977600000000000000000000000	0.844878399999999900000000000000	1610376293209.049000000000000000000000000000
2021-01-11 14:44:53.266740967	-0.037384000000000000000000000000	-3.110348800000000000000000000000	1.031798400000000000000000000000	1610376293266.741000000000000000000000000000
2021-01-11 14:44:53.285971736	0.186920000000000000000000000000	-3.110348800000000000000000000000	1.495360000000000000000000000000	1610376293266.741000000000000000000000000000

accel_np = df_accel.to_numpy()
times = (df_accel.timestamp-df_accel.timestamp.iloc[0])
print(np.shape(accel_np))
plt.figure(1)
plt.subplot(311)
plt.plot(times,accel_np[:,0])
plt.title('Accelerometer X')
plt.subplot(312)
plt.plot(times,accel_np[:,1])
plt.title('Y')
plt.subplot(313)
plt.plot(times,accel_np[:,2])
plt.title('Z')



gyro_np = df_gyro.to_numpy()
times = (df_gyro.timestamp-df_gyro.timestamp.iloc[0])
print(np.shape(gyro_np))
plt.figure(2)
plt.subplot(311)
plt.plot(times,gyro_np[:,0])
plt.title('Gyroscope X')
plt.subplot(312)
plt.plot(times,gyro_np[:,1])
plt.title('Y')
plt.subplot(313)
plt.plot(times,gyro_np[:,2])
plt.title('Z')

(7521, 4)
(7521, 4)





Text(0.5, 1.0, 'Z')



11-Mar-21 12:30:25 | WARNING | findfont: Font family ['normal'] not found. Falling back to DejaVu Sans.

Analysis (coming soon)

Recommendations

• nbdev docs

Install collapsible headings and toc2

There are two jupyter lab extensions that I highly recommend when working with projects like this. They are:

• Collapsible headings: This lets you fold and unfold each section in your notebook, based on its markdown headings. You can also hit left to go to the start of a section, and right to go to the end
• TOC2: This adds a table of contents to your notebooks, which you can navigate either with the Navigate menu item it adds to your notebooks, or the TOC sidebar it adds. These can be modified and/or hidden using its settings.

Export

from nbdev.export import *
notebook2script()

Converted 00_core.ipynb.
Converted 01_dataset.ipynb.
Converted 02_model.ipynb.
Converted 03_spectra.ipynb.
Converted 04_metric.ipynb.
Converted 05_report.ipynb.
Converted 06_cognitive.ipynb.
Converted 07_heartrate.ipynb.
Converted 08_summary.ipynb.
Converted Experiment1.ipynb.
Converted Experiment2.ipynb.
Converted Experiment_BehaviorVisualization.ipynb.
Converted Experiment_Muse_HR.ipynb.
Converted index.ipynb.