Monday, November 19, 2012

Raspberry Pi Home Datalogger

I've wanted to do something like this since I first started playing with microprocessors.  The idea of an inexpensive, distributed sensor network throughout the house is really cool.  In Hollywood we always see someone sitting at their computer console accessing their security system.  It's typically a wire-frame display with sensors all over the place.  They're getting all kinds of data, and even providing the occasional remote output (displays, lights or sirens, etc).

The $35 Raspberry Pi is almost the ideal basis for this kind of sensor network.  It runs a (relatively) well developed Linux distribution.  It has two USB ports, runs on 5v, sports an ethernet port, and will support almost any video display out there.  More importantly, it has several exposed general purpose I/O pins and supports I2C.

I'm using Lady Ada's Occidentalis distro.  So far it has been incredibly stable (though it swaps between video outputs if I cut power to the system).  I'm using this distro because there are examples using Python to access the various GPIO's and the I2C.

My previous post detailed some of my earlier experiments with the system.  Since then, I have worked on building a series of programs to access a BMP085 board attached to the I2C bus.  I haven't done much with Python in quite awhile, so I'm fairly rusty and lacking a definite style.

I finished a series of programs last night that check the sensor, log the sensor data to a logfile and update a webpage, and a simple program to automate the whole process.  Currently I've got the sensor being checked and logged every minute.  The logger program is using the Python Logging module.  I'm recording the event level (I'm generating a warning if the temperature reaches 30c), the epoch time (to facilitate graphing later), and the temperature and pressure (I don't care about the altitude).  Using epoch time versus Python's asctime also saves some memory.  The log files are between 1.8 and 18 megabytes per day (one measurement per minute).  This yields recordings between 50-500 days per gigabyte.  I'm not sure why there is such an insane difference between "Total Size of Files" and "Size on Disk".  Given that it's close to an order of magnitude, I need to address that at some point.

I'm looking to increase the number of sensors on the board.  I'm playing around with a GY-80 board that I got off of eBay some time ago.  It includes the BMP085 sensor, plus an IMU/Gyro component with a compass.  It was about $20.  I'm wondering if the resolution is tight enough to work as a seismograph, though I'll have to increase the polling rate to something much higher than once a minute.  Luckily, with the processing power of the Raspberry Pi, I could poll the sensor very quickly, analyze the data locally, and only report data that was relevant.  This idea is going to be an add on after some of the other to-do list is achieved.

A big thank you to the write of the Giuseppe Urso Blog.  He's found the datasheets for all of the components on this board (I think).  The ebay seller has not been able to provide good information for me.

Things to do:
I want to improve the webpage.  Right now it's a simple Apache text page that shows the temperature and pressure, along with the system time of the latest measurement (actual time, not epoch time).

I want more sensors.  I'd like a light and motion sensor (again, we're trying to get close to that Hollywood sensor system).  It would be great to incorporate a smoke/carbon monoxide/gas sensor into this build.  A networked, web-enabled hazard detector would be incredible.  I've already got a couple of sensors for this. To get them to work, I need to grab something that will let me add analog to digital feeds to the board (perhaps this?).

I really think I'd like to incorporate a second temperature sensor.  I'd like my first sensor node to be located just inside the front door.  Running a cable outside to a sensor (MPL115A2) would be pretty easy, and would give me the ability to log the weather outside compared to the environment inside.  The capability would also be nice if Angel decides to start working with herps again.  This would allow us to monitor the inside and outside of the tank.

The webpage needs serious work.  I'd like to be able to generate graphs of the data, on the fly (click on the parameter, and it brings up a graph of the last hour.  Click on that graph it shows the last 12 hours.  Click on that, it shows the last day.  Week, month, year, etc).  My skills with Python are not up to the task yet.  Hell, my skills with HTML are essentially non-existent (My webpages in the past have all used Dreamweaver).  I need to see if I can merge the two, and someone get the Python code to play nicely with a Dreamweaver generated page.

Automated alerts.  We'll go back to the Hollywood example for this one:  When the bad guys are breaking in, I need the network to tell my cellphone (or bring up an alert on my computer).  A more practical concept:  When the house gets too hot, I need to be told.  When the house is on fire, I need to be screamed at.

I want to keep the cost down.  The average cost, per node, should be less than $100.  At this price point, folks can afford to pick up a couple of nodes to watch their doors.  As they like it more, they could grab additional nodes for other rooms in the house (I want to be able to control my small home theater system using my cellphone and an IR equipped node).

Webcam support.  The Pi has two USB ports.  Once the node is developed, there is no reason to have the USB ports in use.  A web cam is a cheap (I saw a couple for under $10 the other day) way to gain tremendous amounts of information about a locale.  Even if the camera is only used to snap stills to send to a remote site (or just log locally) the idea has tremendous value.  As it stands, I haven't even tried hooking up a camera to the USB ports.

Free and open code.  An idea like this is only as usable as the guy making everything.  I'm not an engineer or computer scientist.  If I could get a couple of those guys interested in the project, they'd be able to do incredible things with it.  More to the point, they'd see ideas that I'd never even consider.  This project, as an open source project, has real potential.  I'm going to work on setting up a GitHub account, and making my code public (I'll warn you, it's ugly code).

I'll post up more as I get it.

Late edit:  I'm starting to look at Lady Ada's Raspberry Pi WebIDE.  I spent the afternoon/evening learning BitBucket, and now I've got a BitBucket account with the code on it (PiLog).  I may not be doing things correctly, so the repository may be a little bizarre over the next couple of days.  The code that was loaded tonight was tested to work, though your mileage may vary.

Monday, November 12, 2012

Ultrasound Phantoms: War were declared

The ultrasound phantoms work.  They have a few limitations, but for certain applications, these cheap DIY phantoms are going to be far superior to expensive commercial phantoms.  In fact, part of their DIY nature makes them inherently superior.  Creating a phantom for a special purpose, such as vessel cannulation, foreign body identification, or needle procedures, is simple.

One of the big issues that has come up is bacterial/fungal growth on the phantom.  This should be expected, as the phantom is constructed of gelatin and sugar-free psyllium.  The system is essentially a giant petri dish.  I needed to find a way to inhibit microbial growth.  Not just inhibit, but stop.  Completely and totally.

I lucked out in a couple of ways.  I tried mixing some bleach into the material when it was on the stovetop.  The mixture foamed up a fair amount.  This wasn't a big issue with the first two layers, as pouring the next layer seemed to dissolve the previously settled foam.  The final layer settled with a very large amount of foam.  This foam is a random mixture of air and gelatin, and almost completely sono-opaque.

This is the external surface of the simulant, and represented a major problem for the phantom.  It was impossible to image past this interfering layer.  I tried scraping the surface foam off, but to no avail.
I spent three shifts at the hospital trying to find a way to make the system workable.  At this point I had intentionally inoculated the surface with dust and dirt to attempt encourage microbial growth. At the three day point, no growth, but no apparent solution.

Ending my shift one morning, I had my "Eureka" moment.  One of the workmen was removing floor tiles by heating them with a propane torch.  Between my broken Spanish and his broken English, I was able to convey that I wanted to borrow his propane torch.  I quickly heated the surface of the phantom, melting the top foam layer.  It liquified and appeared to completely remove the foam layer.

I waited ten anxious minutes, visibly bouncing.  I placed the ultrasound transducer and was rewarded with two easily visible vessel simulants.  Cannulation was almost exactly the same (the new material seems somewhat more friable).

Six weeks later, the phantom was still visibly free of microbial growth (I don't have the patience or material to actually test for microbial growth beyond naked eye visualization).

I'm stuck at the next step.  I'm either casting a human arm and making a mould, or I'm developing some method to snake the vessels through the simulant to increase the difficulty in cannulation.

Tuesday, November 6, 2012

Overdue Updates

For my one reader (Thanks Mom!) I know the updates for the Ultrasound Phantoms are overdue. There is progress. Unfortunately, you don't get to read about it today.

 A couple of months ago I read about this cool new computer, the Raspberry Pi. As far as I know, they've only shipped the model B board, which is $35. That money gets you a Linux computer that is slightly bigger than a credit card. You need to supply a keyboard, SD card, and that's really it. If you want to run a Windows-like GUI, you'll want to have a mouse as well. It's got a couple of dozen general purpose I/O pins to let you build in your own gadgets and stuff (Read a pushbutton, blink an LED, etc).

 The board supports at least half a dozen types of Linux. I went with the Adafruit Occidentalis build. It's build off of Debian Linux, with some added extras, This incorporates libraries for SPI, I2C, One Wire, and WiFi built right into the distro. Couple this with the already included Python (Version 2.7 and Version 3.2) and you have a junior hacker's dream.

 I'll reiterate: $35. I had everything else lying around the house (SD card, spare keyboard and spare mouse). I have a computer that will hook up to pretty much any video display I'll run into. It supports HDMI 1080p right out of the box. It plays nice audio. It surfs the web (slowly, sometimes). For less than the price of a copy of Windows, a new video game, or a tank of gas (holy crap! Yeah, and I drive a Prius).

 It's Linux. For some people that will be a deal breaker (Again, less than the cost of...). I'm having to relearn a fair amount. I used Linux a couple of times, years ago. I had a Linux box once, to toy around with. I had a dual boot netbook where I utilized Ubuntu to run some network diagnostics.

This time around, I'm really focusing on the command line interactions. The little gizmo is decent with the GUI but it does slow down a fair amount at times. However, this thing screams from the command line.

 I'm re-discovering Python as well. I learned 2.7 during college (Thank you, Dan Fleck. You got me excited about programming, and changed my life). It looks like there is a serious attempt to use Python 3 in the Raspberry Pi world.

 I wrote a quick utility to poll the Adafruit Pi Cobbler pin-breakout board. Eventually I want to get the pin states over a network.
import RPi.GPIO as io 
for i in range (26): 
                    print('invalid pin ')

I'm running the program over SSH, so I guess, technically, I'm checking the pin state over the network.

It's important to note:
First, you have to run the program with superuser permissions (sudo).
Second, the program numbers the pins differently than the pins are numbered on the Adafruit breakout. Third, you probably need to be REALLY careful with this code. It attempts to mess with all of the pins, some of which aren't GPIO pins. So far, it doesn't seem to have bothered anything.

I'm waiting for some more parts so that I can start messing around with I2C sensors. Eventually I want to build an environmental monitoring system.