Scripts to read stats from a Massimo Rad 8 pulse oximeter and push to elasticsearch for visualization via grafana, etc
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README.md
REINSTALL-onion.txt
create_index_and_mappings.sh
curl_docs_to_es.sh
read_pulse_ox.sh
sample-grafana-dashboard.json
tail_log_file_and_curl.sh
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README.md

"Glue code" for reading stats off of a Massimo Rad 8 pulse oximeter and pushing them to elasticsearch to view them in Grafana.

YouTube video showing my setup in action

https://youtu.be/t2B6XVP6vvs

Background:

This writeup mostly assumes basic familiarity with Linux. If you haven't worked with Linux before, you might want to find a friend who has. (I'm happy to answer questions as I have time...reach me at twitter.com/yahnatan.)

Materials:

  • one Massimo Rad8 pulse oximeter with 9-pin serial port on the back
  • one microcomputer (Onion Omega2, Raspberry Pi 3, BeagleBone Black, or another Linux-based microcomputer with wifi, preferably with battery-powered option)
  • one serial-to-USB cable (I used a Sabrent CB-DB9P USB 2.0 to Serial 9-Pin DB-9 RS-232 Converter Cable) which you will connect from the serial out port on your Massimo Rad8 to the microcomputer
  • one regular computer (Windows, Linux, or Mac) which stays running on your home network all the time to act as the "server"; onto it you will install some free database and visualization software which will then be viewable from any device on your home network with a web browser.

Caveats and tips:

  • These scripts are pretty rough (e.g. a few assumptions, unnecessarily writing data to disk, not very resilient) and are more intended to serve as an example.

  • If you're also thinking about experimenting with home automation (something I highly recommend for people w/neuromuscular disabilities), I recommend considering Samsung SmartThings, as its open API makes it easier to connect custom devices. I have a Samsung device driver for the Massimo Rad8 which allows us to connect my son's pulse ox to our home automation system for extra visibility (and hopefully, eventually, device triggers / rules like "blink lights if he's asleep and heart rate goes above 140").

Connecting to your Massimo Rad 8 pulse ox

You will need a serial-to-USB cable. I used a Sabrent CB-DB9P USB 2.0 to Serial (9-Pin) DB-9 RS-232 Converter Cable. Keep in mind when you buy: I have heard reports of the serial end being too bulky preventing a good connection to the pulse ox serial port.

If you connect that cable between the Rad8 and your microcomputer, it should get mounted at /dev/ttyUSB0 (or similar).

$ cat /dev/ttyUSB0
02/22/16 22:47:45 SN=0000056661 SPO2=098% BPM=097 PI=03.60% SPCO=--.-% SPMET=--.-% DESAT=-- PIDELTA=+-- ALARM=0000 EXC=000800

02/22/16 22:47:46 SN=0000056661 SPO2=098% BPM=096 PI=03.95% SPCO=--.-% SPMET=--.-% DESAT=-- PIDELTA=+-- ALARM=0000 EXC=000800

02/22/16 22:47:47 SN=0000056661 SPO2=098% BPM=096 PI=04.25% SPCO=--.-% SPMET=--.-% DESAT=-- PIDELTA=+-- ALARM=0000 EXC=000800

02/22/16 22:47:48 SN=0000056661 SPO2=098% BPM=096 PI=03.19% SPCO=--.-% SPMET=--.-% DESAT=-- PIDELTA=+-- ALARM=0000 EXC=000800

02/22/16 22:47:49 SN=0000056661 SPO2=098% BPM=097 PI=02.41% SPCO=--.-% SPMET=--.-% DESAT=-- PIDELTA=+-- ALARM=0000 EXC=000800

If after hooking up the Rad8 to your computer, you don't see any output, see below for troubleshooting tips.

How to use:

# set up your elasticsearch index (run this one time)
$ ./create_index_and_mappings.sh my-childs-med-data server-running-elasticsearch:9200

# after you've plugged in your pulse ox via a serial-to-USB cable
$ ./read_pulse_ox.sh /dev/ttyUSB0 ~/data.out

# start piping data to elasticsearch
$ ./tail_log_file_and_curl.sh ~/data.out

Setting up Grafana:

Follow the instructions for setting up Grafana -- currently at http://docs.grafana.org/install/.

For your datasource, find/follow the instructions for elasticsearch.

Once you've set up Grafana, go to the Grafana URL in your browser (probably something like http://192.168.1.5:3000, where the 192.168.1.5 is the IP address of the computer running Grafana). Click log in.

Select Dashboards > Import and click the "Choose File" button under "Import File."

Load up the sample-grafana-dashboard.json file I included with this project.

IMPORTANT: this dashboard is not an equivalent replacement for the Massimo Rad8 itself! The Rad 8 is a certified lifesaving medical device. Use this dashboard to extend visibility and tracking, but do not rely on it in the way you would depend on the Massimo itself, as it is not "failsafe" and could fail in any number of places (e.g the remote device reading the stats, the server hosting elasticsearch, elasticsearch itself, grafana, your web browser, or the web client).

ADDITIONAL CAVEAT: the "current" SPO2 and HR values in my sample dashboard are intended to match the values on the Massimo Rad 8 itself. Thus, they average over an 8-second period. However, they are actually on a 30 second delay. This is because over time, the internal clock of the pulse ox gets slightly off. Every few weeks to months or so you may need to enter the settings of the pulse ox and update the clock. Otherwise, even if all your computing devices have their times synced up via an online time server, you may start to see a weird "delay" in the numbers posting.

Tips/Troubleshooting:

  • If, after hooking up the serial port of your Rad8 to your input device, you don't see any output from the pulseox at /dev/ttyUSB0 (or similar), you may need to change the setting on your Rad8 serial port output from the default value of ASCII 2 to ASCII 1. From the Masimo Rad8 User Manual (available online if you do a Google search):

    To access Level 3 parameters/measurements, hold down the Enter Button 
    and press the Down Button for 5 seconds. After entering menu Level 3, 
    use the Up or Down button to move between settings.
    

    The setting you're looking for is Serial Output (SEr), and you want to change it to ASCII 1 (AS1).

    IMPORTANT: your child's pulse oximeter is a life-saving device. If you change the wrong setting inadvertently, you could seriously compromise the safety of your child and/or make yourself totally liable for the consequences. Don't change settings unless you're confident you know what you're doing.

  • If after changing your Massimo Rad 8 to AS1 setting, you still don't see data coming in when you call cat /dev/ttyUSB0 (or wherever your serial-to-USB cable mounts to), it may be because the data is being buffered in Unix pipes. This is something that can be manipulated (and in issue #1 in this project there is an example of how to do this in Python).

  • You will want to make these scripts run automatically at startup. On my Onion Omega, I did this by adding the following to /etc/rc.local:

    # Put your custom commands here that should be executed once
    # the system init finished. By default this file does nothing.
    cd /root/pulseox
    /root/pulseox/tail_log_file_and_curl.sh /dev/ttyUSB0 192.168.1.6:9200
    exit 0
    
  • You might need to change /bin/bash to point to /bin/ash if, for example, you're using an Onion Omega.

  • You may want to set up a cron job to periodically clear out the on-disk data file (to avoid filling up your disk eventually), e.g.

    0 * * * * echo "" > /root/pulseox/data.out
    
  • Sometimes the USB port will cut out unexpectedly. This is due to some sort of current override feature which is part of the USB spec. One way to fix this is to run the following command (and then reset your connection to /dev/ttyUSB0):

    $ rmmod ehci_platform && modprobe ehci-platform
    
  • If data stops displaying properly in Grafana around the time of daylight savings time changes, going into the settings on your pulse ox (see above for Massimo Rad8 instructions) and changing the hour manually should bring things back into alignment.

Understanding the Massimo's ALARM codes

From the Massimo Rad 8 User Manual (http://www.ontvep.ca/pdf/Masimo-Rad-8-User-Manual.pdf):

Trend Data format
The exceptions are displayed as a 3 digit, ASCII encoded, hexadecimal
value. The binary bits of the hexadecimal value are encoded as follows:
000 = Normal operation; no exceptions
001 = No Sensor
002 = Defective Sensor
004 = Low Perfusion
008 = Pulse Search
010 = Interference
020 = Sensor Off
040 = Ambient Light
080 = Unrecognized Sensor
100 = reserved
200 = reserved
400 = Low Signal IQ
800 = Masimo SET. This flag means the algorithm is running in full
SET mode. It requires a SET sensor and needs to acquire some
clean data for this flag to be set

Correlating the above exceptions to the actual ALARM or EXC codes from your Massimo Rad8 requires a little close reading and mathematical thinking. Let's look at some example data.

Here is a sampling of over 2 million ALARM data points from over two months of collection from my son's Massimo Rad8:

ALARM # times appeared
000 2 Mil
020 56 K
032 3 K
010 2K
012 1K
030 726
03a 623
038 184
018 10
01a 9
014 8
034 1

Based on these numbers, it makes sense that ALARM=000 means "Normal operation", aALARM=020 means "Sensor Off" (our most common alarm situation), and ALARM=010 would mean "Interference" (another seemingly common occurrence). However, values like 032, 03a, etc don't appear in the above table. What gives?

Re-reading the description above, I note that it says "the binary bits of the hexadecimal value are encoded." Notice as well that each of the hex values in the table from the manual correspond to a single bit in an 12-digit binary string:

ALARM HEX BINARY
Normal 000 0000 0000 0000
No sensor 001 0000 0000 0001
Defective 002 0000 0000 0010
Low Perf 004 0000 0000 0100
Pulse Search 008 0000 0000 1000
Interference 010 0000 0001 0000

And so on.

The power of this scheme is that any combination of alarms can be represented in a single hexadecimal number, because any of the hexadecimal values in their table can be summed with any other values to create a totally unique sum. That unique sum can then be decomposed back into only one possible set of sums. For example:

Example: Sum = Code 1 + Code 2 + Code 3 + Code 4
In HEX: 03a = 020 + 010 + 008 + 002
In binary: 0011 1010 = 0010 0000 + 0001 0000 + 0000 1000 + 0000 0010

(Note that I've dropped the leading 0000 from each of the binary values to keep the entries from wrapping. But check the math -- it works!)

Using this approach, the other alarms from my son's data can be decoded as follows:

ALARM CODES INTERPRETATION
032 020 + 010 + 002 Sensor Off + Interference + Defective Sensor
012 010 + 002 Interference + Defective Sensor
030 020 + 010 Sensor Off + Interference
03a 020 + 010 + 008 + 002 Sensor Off + Interference + Pulse Search + Defective Sensor
038 020 + 010 + 008 Sensor Off + Interference + Pulse Search

Additional tips:

I am using https://github.com/rocketinventor/web-page-screensaver to bring the default medical monitoring dashboard up on the screen of the computer in my son's room. I also set one corner of the screen as a "hot corner" to activate the screensaver,so that any of my son's caregivers can quickly bring the Grafana monitoring dashboard back up.

Currently our setup is only visible within our home network. However, another parent told me about http://www.no-ip.com -- a free service which sjould let me access our server from outside my home network.

Credit where credit is due:

Inspired by http://www.instructables.com/id/Pulse-Oximeter-Data-Capture-with-Raspberry-Pi/

Massimo alarm codes from nmenon at https://github.com/nmenon/masimo-datacapture/blob/master/masimo-capture.py#L249

View my setup at https://youtu.be/t2B6XVP6vvs

A quick intro to the Onion Omega for someone who doesn't have one: http://www.hanselman.com/blog/PlayingWithAnOnionOmegaIoTDeviceToShowLiveBloodSugarOnAnOLEDScreen.aspx (If you have an Onion Omega, I recommend the tutorials from Onion; they're pretty great!)

Questions? Comments? Please contact me!