Epilepsy (Seizure Detection / Alarm) Information

 I had forgotten that this blog existed so have not posted to it for quite a while....

Most of my recent work has been on Epilepsy with the OpenSeizureDetector project.

The source code for that is all on Github:  https://github.com/openseizuredetector.

DIY Gas Chromatograph

Why Bother?

A while ago I started looking at making a biogas generator, but didn't commission it because I had no way of detecting what gases were coming off it.   A few weeks ago I was inspired by someone showing that they had made a DIY gas chromatograph, so thought that if I made one, we could do real experiments on biogas production from household waste to see what works best etc.....

So, our litle project for this Christmas holiday was to make ourselves a DIY gas chromatograph and see if we could use it to detect the difference between CO2 and Methane, which are the two main products I expect to see from the fermentation to produce biogas.

Note that when I talked to some chemists about this they advised that I could do this much more easily using wet chemistry because of the significant differences between CO2 and Methane, but I am a physicist, so something using physical properties sounds much more fun!   (It is also much more of a useful education project for Laura, but she didn't know that at the start).

The Principles

A gas chromatograph relies on a constant flow of carrier gas passing through a 'column', which is in a temperature controlled oven.    You inject the sample gas into the flow at the inlet of the column, and the constituent parts travel through the column at different rates, so the different constituents come out of the column at different times after injection.  See pretty picture from wikipedia article below.

Components of a DIY Chromatograph

Infrastructure

The infrastructure (temperature measurement, temperature control, detector control etc.) can be done using an arduino microcontroller.

Arduino Based Temperature Controller

This was Laura's part of the project - she developed an Arduino programme (sketch) that does the following:

• Measures the resistance of thermistors (assuming they are wired as a potential divider).
• Converts the resistance to temperature in degC.
• Performs 3 term (PID) temperature control by varying an 'analogue' output pin to control the oven temperature (see below for oven details).
• Outputs relevant data (temperatures etc.) to the controlling computer using the USB serial connection on the arduino.
• Responds to commands from the USB serial line to change set point, PID gains etc.

The Arduino Code is here: https://github.com/jones139/arduino-projects/tree/master/gc/oven.

User Interface

We had a difficult design choice for user interface - do we write a 'native' user interface on a computer connected to the arduino, or make a web based system?

I decided to go for a web based system, which means that you can use any computer as the user interface, so we need a little web server.   Although some people use Arduino's for this, I thought it would be much easier to use a Raspberry Pi.

We re-cycled the web server code from our Seizure Detector project, which is a simple python web server.

The python programme does the following:

• Listen for web requests.
• If no special commands are given, it serves a simple page showing the chromatograph settings and a graph of the temperature history (which will also be the detector output). 
• The main web page includes javascript code to allow bits of it to be updated without refreshing the whole page every time (the html/javascript code is Laura's).
• Respond to specific commands (such as change set point) by sending these to the arduino across the serial line.
• Collect data from the arduino (it sends a set of data every second), and create at time series.
• Use the time series data to plot a graph of temperature history etc.

The web server code is the python files here: https://github.com/jones139/arduino-projects/tree/master/gc  (execute runServer.py) to start the web server.

The html and javascript based user interface is all here: https://github.com/jones139/arduino-projects/tree/master/gc/www.

The infrastructure part went well - we have a web interface to a three term temperature controller that works fine, and sends data back to the web server, which produces a graph of the temperature history.  You can change set point, controller gains etc over the web interface.

Power Supply and Case

We will need a variety of power supplies (5V for the Raspberry Pi, 12V for heaters, mains for the pump).   I had an old computer case in the Attic, so we used that - it has a power supply that gives 5V, 12V high current, +/-12V and 3.3V, so plenty for what we need.    The case will also house the finished instrument so it will look neater than most of my projects once I put the lid on!

The case for the project!

Case before I removed the old computer boards to make room. - the power supply is at the back.

 The ATX power supply does not start up when the unit is powered on - you needed to press the on button on the case, which energised a line to the power supply via the main computer board.   You can force the power supply to run by shorting a particular pin on the main connector down to ground:

Carrier Gas

To keep things simple I propose to use air as the carrier gas, and use a fish tank air pump to push it through the column.    Because it is a bit noisy, we made the Arduino and web interface allow you to switch it on and off easily.  The pump is mains powered so we used a solid state relay to switch it on and off, and covered the mains connections with plastic to stop us blowing ourselves up with loose wires in the case...

The air pump with sample injector syringe.

Solid state relay mounted in bottom of the case - all the mains connections are covered in clear plastic to avoid them contacting low voltage parts of the equipment.

Oven

For the oven we need an insulated case and some heaters.   For the case we used the old CD drive case from the computer, because it fits in the computer case neatly:

We added some polystyrene insulation to the top to reduce heat loss, and a bit of bubble wrap to the bottom (could not get too much in, or there would be no room in the oven....

The heater element is an aluminium plate cut to the size of the oven with three resistors bolted to it.

A power transistor is also mounted in the case to switch the current flow to the resistors.  This means that the 12V power supply only has to go to the oven, and we can provide a 5V switching signal from the arduino to control the heater using the transistor:

Heater plate with resistors attached, along with power transistor to control the heater current.   Note that we had to disconnect the transistor heat sink from the plate because grounding it to earth switched on the transistor, so we had an over-heat fault on first commissioning - the arduino tried to switch off the heaters, but they continued at full power - at least we proved that we can get the oven to just over 90degC...

Circuit diagrams for the thermistor measurement and the heater control circuit.

Detector

The detector is my part, and is the bit that is holding up the project at the moment!

First Version - heat loss to environment

My first go was to rely on the gas coming out of the oven being hot, and looking at the amount of cooling of the sample gas compared to pure carrier gas as it passed through some copper tubes:

Unfortunately the gas flow rate is so low that the gas has cooled to ambient temperature before it gets to the detector, so I can't measure anything useful, so need a re-think.

Second version - heated constantan wire

Next, try a hot wire detector - loop of constantan wire used to heat a thermistor using a constant current source - the temperature above ambient should depend on the thermal properties of the gas surrounding it.

Here my lack of practice at electronics design let me down - I made a high current source using a trusty (>30 year old) 741 op-amp and a power transistor.   

Arduino, along with 741 and power transistor current source (the sense resistor is the big grey cylinder above the arduino).  The things in the crocodile clip are the heated and ambient thermistors.

Unfortunately I was using a 100R resistor to sense the current, and my loop of constantan is only about 1R.   This meant that I put a lot more power into the sense resistor than my 'hot' wire - no detectable increase in wire temperature, but smoke and a warming glow from the sense resistor....   Replaced it with the more robust resistor shown in the picture above, which acts as a nice room heater, but no measurable heating of the thermistor.

So, need a higher resistance heater for the thermistor - think I will dismantle a 12V light bulb next....

Summary

Quite an interesting holiday project, but not finished.  

What went well:

• Working web interface to an arduino temperature controller
• Working web based data logger.
• Working oven and switchable pump.
• Nice case with useful power supply.
• Laura learned to programme an Arduino, and write javascript web pages

What didn't go well:

• The detector!
• I am out of practice at electronics design, and mis-judged heat losses from very very low gas flow rates!

Alternative Operating System (Cyanogenmod) on Samsung S4 mini

My Samsung S4 mini Android mobile phone works very well, but it keeps running out of internal storage space for applications, so in practice I can not have very many of my own applications on the device.

I realised this is because the phone came with a lot of applications pre-installed, which keep getting updated, and the updates take up storage space (in addition to the factory installed version, which is not replaced).   And I don't use most of the applications that are installed on it - no need for things like Google Maps when you can use OsmAnd navigation etc. whcih uses OpenStreetMap data so is more detailed.

So tonight I decided to try installing cyanogenmod, which is another build of Android that can replace the factory firmware.    I found this a bit nerve wracking because I was doing it as a bit of a 'black box' - download this file, press these buttons etc.   There are also several versions of a S4 mini (mine is a GT-I9192, which seems to be less common).   If I were doing it on a Windows computer I would be very worried about viruses etc. - still nervous about the firmware that I have downloaded - might try to build it from source another day to give me a bit more confidence.

The end result is my phone seems to work, running cyanogenmod 11, which is good

Don't treat this as instructions of how to do it - it is just my notes so I can remember.

Recovery Image
The S4 mini has a recovery mode, which seems to be a very small operating system.   You need a replacement for this which will let you do more  things (like backup your existing firmware before you start anything more serious).
There are a few different alternative recovery systems around, but the one I found that claims to work on an I9192, is called 'Philz' which is a more advanced version of one called 'clockworkmod'.

I got the latest version of Philz recovery from the link here.    And loaded it onto the device using the 'heimdal' software running on my xubuntu linux laptop (I just used the ubuntu packaged version rather than building from source) - I did this by following the instructions here.

It is now possible to boot the phone into recovery mode by pressing the Volumme Up, Home and Power buttons when booting.

Install Cyanogenmod
The extra worrying part is that you need the version of cyanogenmod that matches your phone (not sure what will happen if you don't, but it might take a bit of recovering from...).   I searched the internet to find an unofficial version for my phone (GT-I9192), and got the latest version from here, which is referenced from a post on the xda developers forum.

This went surprisingly smoothly - you can set the recovery program to install a 'zip' image from sideloader, and send the image using 'adb sideload '.

Re-booted and the phone works again, phew!.

Google Apps
One issue with the 'stock' cyanogenmod is that it does not include any of the propriatory google applications, in particular I wanted GMail, Google Plus and the play store.
While it is possible to back them up from the factory firmware, and then restore them into cyanogenmod, you can get pre-packaged versions on the internet (may be issues with licencing here I suspect...), which are packaged as 'gapps' and can be loaded as a 'zip' file the same way as cyanogenmod.

This now gives me a working gmail etc., and i can install other apps like osmand, national rail etc. using play store.

Unfortunately I have installed loads of other google apps that I don't really want, which slightly defeats the object of  going to an alternative firmware - I might have to look at doing the backup and restore bit myself and being more selective about what I back up....

So, I think I have got back to a working phone - I'll have to test it a bit this week before I go travelling again and need it more.

Charity Document Management System

After a bit more development of the Document Management System for our Academy Charitable Trust (HDMS), I have now got something working which I think is useable.    There may well be some changes once we use it in anger for a while and find some 'features' annoying!

Background

HDMS is a Document Management System that has been developed for Hartlepool Aspire Trust (Catcote Academy).

It has been developed because the Trust is expected to have many policies to ensure compliance with statutory regulations, and these policies are implemented within the trust using procedures for detailed instructions, and forms to record information.

It is important that the latest versions of the Policies, Procedures and Forms are available to staff and key stakeholders, and that changes between versions can be tracked and communicated to stakeholders so they know what has changed when a new document is issued.

User Interface

HDMS has been developed to store the Trust's documents in a single repository (a web server) and present the latest version of documents to interested parties. Users are initially presented with a graphical summary of the document structure.
 The user clicks on parts of the graphical summary to search for specific types of documents (such as Financial Procedures, or Human Resources Policies). This gives a list of documents, showing the latest revision number with date of issue, with clickable icons to download either the PDF version or native version of the file.
Authorised users have options to create new revisions, or edit existing draft documents.

Draft versions of documents are not publicly visible, but can be viewed by authorised users. Approval and issue of documents is managed by the draft document being sent electronically to reviewers/approvers.
The document is issued and becomes the latest version once all the reviewers/approvers have approved the document.

The workflow for creating, revising and approving a document is shown in a set of slides here.

The system stores both 'native' (e.g. MS Word) documents and PDF documents. By default the PDF version is delivered to the public, as this can not be modified accidentally. The system can also store 'extra' files, which may be the source files for drawings or tables of data that are used in the document - this is useful for future updates so the author can obtain all the data used to produce the original document.

Live Version

The live version of the system is running at (http://catcotegb.co.uk/hdms).

The software is quite general so may be of use to other small and medium size organisations who wish to manage their documentation in a systematic way. There is a demonstration version of the system available for testing at http://catcotegb.co.uk/hdms_demo - login as 'user1' with password 'test').   The source code is available on my GitHub repository.

Please let me know if you are interested in using this for your organisation and I will help explain how to set it up, because my installation instructions may not be complete!

Academy Charitable Trust Document Management System

Last year our school converted to an academy.   To help us with the set-up of the administrative side of the new organisation, I set up an electronic document management system to hold our management documents such as policies and procedures.

The system I set up was a modified version of OpenDocMan.   This has worked pretty well from the point of view of recording the documents and allowing us to retrieve the issued version, but now we are looking at updating some of the documents, and establishing another part of the organisation, we are finding some limitations.   The most significant problem is that the document does not appear publicly while it is waiting for approval - I want the latest issued document to always be available even while we are reviewing and approving the new version.

I decided that rather than modifying my version of OpenDocMan, it is probably better to write an alternative simple system based on an established software framework.

The new Hartlepool Aspire Trust Document Management System (HDMS) is based on the cakephp framework, which makes interfacing with the database, and dealing with internet http requests very simple, and it automatically produced the code to do basic database record creation/deletion etc. automatically, so I only had to do the 'business' logic.

The concepts for the new system and workflow are shown in these slides, and there is a demo installation here.

Breathing Detection with Kinect - A working Prototype Seizure Detector!

The seizure detector project has come forward a long way since I have been using the Kinect.
I now have a working prototype that monitors breathing and can alarm if the breathing rate is abnormally low.   It sends data to our 'bentv' monitors (image right), and has a web interface so I can see what it is doing (image below).   It is on soak test now.....

Details at http://openseizuredetector.org.uk.

Breathing Detection using Kinect and OpenCV - Part 2 - Peak detection

A few days ago I published a post about how I am using a Microsoft Kinect depth camera and the OpenCV image processing library to identify a test subject from a background, and analyse the series of images from the camera to detect small movements.

The next stage is to calculate the brightness of the test subject at each frame, and turn that into a time series so we can see how it changes with time, and analyse it to detect specific events.

We can use the openCV 'mean' function to work out the average brightness of the test image easily, then just add it onto the end of an array, and trim the first value off the start to keep the length the same.
The resulting image and time series are shown below:

 The image here shows that we can extract the subject from the background quite accurately (this is Benjamin's body and legs as he lies on the floor).  the shading is the movement relative to the average position.










The resulting time series is shown here - the measured data is the blue spiky line.  The red one is the smoothed version (I know I have a half second offset between the two...).

The red dots are peaks detected using a very simple peak searching algorithm.
The chart clearly shows a 'fidget' being detected as a large peak.  There is a breathing event at about 8 seconds that has been detected too.

So, the detection system is looking promising - I have had better breathing detection when I was testing it on myself - I think I will have to change the position of the camera a bit to improve sensitivity.

I have now set up a simple python based web server to allow other applications to connect to this one to request the data.

We are getting there.  The outstanding issues are:

• Memory Leak - after the application has run for 30 min the computer gets very slow and eventually crashes - I suspect a memory leak somewhere - this will have to be fixed!
• Optimum camera position - I think I can get better breathing detection sensitivity by altering the camera position - will have to experiment a bit.
• Add some code to identify whether we are looking at Benjamin or just noise - at the moment I analyse the largest bright subject in the image, and assume that is Benjamin - I should probably have a minimum size limit so it gives up if it can not see Benjamin.
• Summarise what we are seeing automatically - "normal breathing", "can't see Benjamin", "abnormal breathing", "fidgeting" etc.
• Modify our monitors that we use to keep an eye on Benjamin to talk to the new web server and display the status messages and raise an alarm if necessary.

The code is available here.