FaceHR Save

Here’s the code we used in my video with Steve Mould to extract his heart rate from a video of his face!

It’s very much hacked-together-for-a-video level code, but it does run. If you’d like to clean this up and make it slightly more usable, please feel free to make a pull request. :)

If you want a sample video to test it on, you can download the one we used in the video here!

How to use stattohr.py

• You’ll probably need to install a few Python libraries to make this work, see the import statements at the top of the script.
• Run it with python stattohr.py -f steve-face-hr.mp4 to extract the heart rate from a file.
• It will start by displaying random frames from the video so you can pick a skin colour. Click somewhere on the face, and then press A to show the ‘chroma key’ it’s using, which will display a terrifying black and white image like this: This is looking good—it’s selected most of Steve’s skin!
• Press O for ‘OK’, and it will go through taking the average of the skin-coloured pixels and storing it for processing later. You can press A again which has the dual benefit of making it less terrifying to watch, and speeding things up a bit because it can just display the straight video.
• Once it’s gone through the whole video, it will display a few graphs to check everything worked. These show the raw RGB values (not very informative as the main thing you can see is that skin contains more R than G and B!), the RGB values with moving averages subtracted (explained below), and then YUV values with moving averages subtracted (YUV is commonly used when extracting heart rate from skin).
• Close each graph in turn, and then it will automatically start creating output image files with the magnified colour change superimposed on the skin.

How it works

This code just takes the skin RGB values and subtracts two moving averages: a long-period one of around a second to smooth over gross changes (eg if the subject moves their head) and then a short-period one of a few frames to smooth over how noisy the data usually are and make the output look a bit nicer.

More advanced code uses FFTs to extract heart rate frequencies, or clever machine learning to do the same. I tried the former and found it a bit finicky for use in this video!

What it doesn’t do

With apologies, there are a bunch of commented out or otherwise unfinished or unusable bits in this code. There are a few missing components for doing this on a live webcam image, but it would be pretty easy to implement. There’s also some code at the bottom which is commented out which just runs a ‘Welch’ analysis to get frequencies from the smoothed RGB data. This works really surprisingly well! But it’s also far slower than real-time, so I actually did this when I got home, and it never made it into the video anyway. :) It would be pretty easy to make this work either optionally after analysing the video or with the relevant command line flag.

How to use ppg-plots.R

This is just a few simple ggplot graphs to show the data more beautifully. It’s meant to be run interactively in RStudio, just for checking stuff out purposes.

It also includes the (very simple!) code to import a file from Polar Sensor Logger which is what we used to get the ECG from the Polar H10.

Credits

Inspired by pyVHR which implements a load of algorithms to extract heart rate in a far more general way than this script does!