Realtime FFT Audio Visualization with Python

I’m no stranger to visualizing linear data in the frequency-domain. Between the high definition spectrograph suite I wrote in my first year of dental school (QRSS-VD, which differentiates tones to sub-Hz resolution), to the various scripts over the years (which go into FFT imaginary number theory, linear data signal filtering with python, and real time audio graphing with wckgraph), I’ve tried dozens of combinations of techniques to capture data, analyze it, and display it with Python. Because I’m now branching into making microcontroller devices which measure and transfer analog data to a computer, I need a way to rapidly visualize data obtained in Python. Since my microcontroller device isn’t up and running yet, linear data from a PC microphone will have to do.  Here’s a quick and dirty start-to-finish project anyone can tease apart to figure out how to do some of these not-so-intuitive processes in Python. To my knowledge, this is a cross-platform solution too. For the sound card interaction, it relies on the cross-platform sound card interface library PyAudio. My python distro is 2.7 (python xy), but pythonxy doesn’t [yet] supply PyAudio.

The code behind it is a little jumbled, but it works. For recording, I wrote a class “SwhRecorder” which uses threading to continuously record audio and save it as a numpy array. When the class is loaded and started, your GUI can wait until it sees newAudio become True, then it can grab audio directly, or use fft() to pull the spectral component (which is what I do in the video). Note that my fft() relies on numpy.fft.fft(). The return is a nearly-symmetrical mirror image of the frequency components, which (get ready to cringe mathematicians) I simply split into two arrays, reverse one of them, and add together. To turn this absolute value into dB, I’d take the log10(fft) and multiply it by 20. You know, if you’re into that kind of thing, you should really check out a post I made about FFT theory and analyzing audio data in python.

Here’s the meat of the code. To run it, you should really grab the zip file at the bottom of the page. I’ll start with the recorder class:

import matplotlib
matplotlib.use('TkAgg') # THIS MAKES IT FAST!
import numpy
import scipy
import struct
import pyaudio
import threading
import pylab
import struct

class SwhRecorder:
    """Simple, cross-platform class to record from the microphone."""

    def __init__(self):
        """minimal garb is executed when class is loaded."""
        self.RATE=48100
        self.BUFFERSIZE=2**12 #1024 is a good buffer size
        self.secToRecord=.1
        self.threadsDieNow=False
        self.newAudio=False

    def setup(self):
        """initialize sound card."""
        #TODO - windows detection vs. alsa or something for linux
        #TODO - try/except for sound card selection/initiation

        self.buffersToRecord=int(self.RATE*self.secToRecord/self.BUFFERSIZE)
        if self.buffersToRecord==0: self.buffersToRecord=1
        self.samplesToRecord=int(self.BUFFERSIZE*self.buffersToRecord)
        self.chunksToRecord=int(self.samplesToRecord/self.BUFFERSIZE)
        self.secPerPoint=1.0/self.RATE

        self.p = pyaudio.PyAudio()
        self.inStream = self.p.open(format=pyaudio.paInt16,channels=1,
            rate=self.RATE,input=True,frames_per_buffer=self.BUFFERSIZE)
        self.xsBuffer=numpy.arange(self.BUFFERSIZE)*self.secPerPoint
        self.xs=numpy.arange(self.chunksToRecord*self.BUFFERSIZE)*self.secPerPoint
        self.audio=numpy.empty((self.chunksToRecord*self.BUFFERSIZE),dtype=numpy.int16)               

    def close(self):
        """cleanly back out and release sound card."""
        self.p.close(self.inStream)

    ### RECORDING AUDIO ###  

    def getAudio(self):
        """get a single buffer size worth of audio."""
        audioString=self.inStream.read(self.BUFFERSIZE)
        return numpy.fromstring(audioString,dtype=numpy.int16)

    def record(self,forever=True):
        """record secToRecord seconds of audio."""
        while True:
            if self.threadsDieNow: break
            for i in range(self.chunksToRecord):
                self.audio[i*self.BUFFERSIZE:(i+1)*self.BUFFERSIZE]=self.getAudio()
            self.newAudio=True 
            if forever==False: break

    def continuousStart(self):
        """CALL THIS to start running forever."""
        self.t = threading.Thread(target=self.record)
        self.t.start()

    def continuousEnd(self):
        """shut down continuous recording."""
        self.threadsDieNow=True

    ### MATH ###

    def downsample(self,data,mult):
        """Given 1D data, return the binned average."""
        overhang=len(data)%mult
        if overhang: data=data[:-overhang]
        data=numpy.reshape(data,(len(data)/mult,mult))
        data=numpy.average(data,1)
        return data    

    def fft(self,data=None,trimBy=10,logScale=False,divBy=100):
        if data==None: 
            data=self.audio.flatten()
        left,right=numpy.split(numpy.abs(numpy.fft.fft(data)),2)
        ys=numpy.add(left,right[::-1])
        if logScale:
            ys=numpy.multiply(20,numpy.log10(ys))
        xs=numpy.arange(self.BUFFERSIZE/2,dtype=float)
        if trimBy:
            i=int((self.BUFFERSIZE/2)/trimBy)
            ys=ys[:i]
            xs=xs[:i]*self.RATE/self.BUFFERSIZE
        if divBy:
            ys=ys/float(divBy)
        return xs,ys

    ### VISUALIZATION ###

    def plotAudio(self):
        """open a matplotlib popup window showing audio data."""
        pylab.plot(self.audio.flatten())
        pylab.show()

And now here’s the GUI launcher:

import ui_plot
import sys
import numpy
from PyQt4 import QtCore, QtGui
import PyQt4.Qwt5 as Qwt
from recorder import *

def plotSomething():
    if SR.newAudio==False: 
        return
    xs,ys=SR.fft()
    c.setData(xs,ys)
    uiplot.qwtPlot.replot()
    SR.newAudio=False

if __name__ == "__main__":
    app = QtGui.QApplication(sys.argv)

    win_plot = ui_plot.QtGui.QMainWindow()
    uiplot = ui_plot.Ui_win_plot()
    uiplot.setupUi(win_plot)
    uiplot.btnA.clicked.connect(plotSomething)
    #uiplot.btnB.clicked.connect(lambda: uiplot.timer.setInterval(100.0))
    #uiplot.btnC.clicked.connect(lambda: uiplot.timer.setInterval(10.0))
    #uiplot.btnD.clicked.connect(lambda: uiplot.timer.setInterval(1.0))
    c=Qwt.QwtPlotCurve()  
    c.attach(uiplot.qwtPlot)

    uiplot.qwtPlot.setAxisScale(uiplot.qwtPlot.yLeft, 0, 1000)

    uiplot.timer = QtCore.QTimer()
    uiplot.timer.start(1.0)

    win_plot.connect(uiplot.timer, QtCore.SIGNAL('timeout()'), plotSomething) 

    SR=SwhRecorder()
    SR.setup()
    SR.continuousStart()

    ### DISPLAY WINDOWS
    win_plot.show()
    code=app.exec_()
    SR.close()
    sys.exit(code)

Note that by commenting-out the FFT line and using “c.setData(SR.xs,SR.audio)” you can plot linear PCM data to visualize sound waves like this:

Finally, here’s the zip file. It contains everything you need to run the program on your own computer (including the UI scripts which are not written on this page)

DOWNLOADSWHRecorder.zip

If you make a cool project based on this one, I’d love to hear about it. Good luck!

 

Permanent link to this article: http://www.SWHarden.com/blog/2013-05-09-realtime-fft-audio-visualization-with-python/

Realtime Data Plotting in Python

Notice

If you’re looking to plot PCM audio or FFT frequency-domain audio data, you might find my next post more interesting. I use a PC microphone as input, and graph the data in real time.

http://www.swharden.com/blog/2013-05-09-realtime-fft-audio-visualization-with-python/

I love using python for handing data. Displaying it isn’t always as easy. Python fast to write, and numpy, scipy, and matplotlib are an incredible combination. I love matplotlib for displaying data and use it all the time, but when it comes to realtime data visualization, matplotlib (admittedly) falls behind. Imagine trying to plot sound waves in real time. Matplotlib simply can’t handle it. I’ve recently been making progress toward this end with PyQwt with the Python X,Y distribution. It is a cross-platform solution which should perform identically on Windows, Linux, and MacOS. Here’s an example of what it looks like plotting some dummy data (a sine wave) being transformed with numpy.roll().

How did I do it? Easy. First, I made the GUI with QtDesigner (which comes with Python x,y). I saved the GUI as a .ui file. I then used the pyuic4 command to generate a python script from the .ui file. In reality, I use a little helper script I wrote designed to build .py files from .ui files and start a little “ui.py” file which imports all of the ui classes. It’s overkill for this, but I’ll put it in the ZIP anyway.  Here’s what the GUI looks like in QtDesigner:

 

After that, I tie everything together in a little script which updates the plot in real time. It takes inputs from button click events and tells a clock (QTimer) how often to update/replot the data. Replotting it involves just rolling it with numpy.roll().  Check it out:

import ui_plot #this was generated by pyuic4 command
import sys
import numpy
from PyQt4 import QtCore, QtGui
import PyQt4.Qwt5 as Qwt

numPoints=1000
xs=numpy.arange(numPoints)
ys=numpy.sin(3.14159*xs*10/numPoints) #this is our data

def plotSomething():
    global ys
    ys=numpy.roll(ys,-1)
    c.setData(xs, ys)
    uiplot.qwtPlot.replot()   

if __name__ == "__main__":
    app = QtGui.QApplication(sys.argv)
    win_plot = ui_plot.QtGui.QMainWindow()
    uiplot = ui_plot.Ui_win_plot()
    uiplot.setupUi(win_plot)

    # tell buttons what to do when clicked
    uiplot.btnA.clicked.connect(plotSomething)
    uiplot.btnB.clicked.connect(lambda: uiplot.timer.setInterval(100.0))
    uiplot.btnC.clicked.connect(lambda: uiplot.timer.setInterval(10.0))
    uiplot.btnD.clicked.connect(lambda: uiplot.timer.setInterval(1.0))

    # set up the QwtPlot (pay attention!)
    c=Qwt.QwtPlotCurve()  #make a curve
    c.attach(uiplot.qwtPlot) #attach it to the qwtPlot object
    uiplot.timer = QtCore.QTimer() #start a timer (to call replot events)
    uiplot.timer.start(100.0) #set the interval (in ms)
    win_plot.connect(uiplot.timer, QtCore.SIGNAL('timeout()'), plotSomething)

    # show the main window
    win_plot.show()
    sys.exit(app.exec_())

I’ll put all the files in a ZIP to help out anyone interested in giving this a shot. Clicking different buttons updates the graph at different speeds. If you make something cool with this concept, let me know! I’d love to see it.

DOWNLOAD PROJECT: realtime_python_graph.zip

Permanent link to this article: http://www.SWHarden.com/blog/2013-05-08-realtime-data-plotting-in-python/

AVR Programming in 64-bit Windows 7

A majority of the microcontroller programming I do these days involves writing C for the ATMEL AVR series of microcontrollers. I respect PIC, but I find the open/free atmosphere around AVR to be a little more supportive to individual, non-commercial cross-platform programmers like myself. With that being said, I’ve had a few bumps along the way getting unofficial AVR programmers to work in Windows 7. Previously, I had great success with a $11 (shipped) clone AVRISP-mkII programmer from fun4diy.com. It was the heart of a little AVR development board I made and grew to love (which had a drop-in chip slot and also a little breadboard all in one) seen in a few random blog posts over the years. Recently it began giving me trouble because, despite downloading and installing various drivers and packages, I couldn’t get it to work with Windows Vista or windows 7. I needed to find another option. I decided against the official programmer/software because the programmer is expensive (for a college student) and the software (AVR studio 6) is terribly bloated for LED-blink type applications. “AStudio61.exe” is 582.17 Mb. Are you kidding me? Half a gig to program a microchip with 2kb of memory? Rediculous.  I don’t use arduino because I’m comfortable working in C and happy reading datasheets. Furthermore, I like programming chips hot off the press, without requiring a special boot loader.

I got everything running on Windows 7 x64 with the following:

Here’s the “hello world” of microchip programs (it simply blinks an LED). I’ll assume the audience of this page knows the basics of microcontroller programming, so I won’t go into the details. Just note that I’m using an ATMega48 and the LED is on pin 9 (PB6). This file is named “blink.c”.

#define F_CPU 1000000UL
#include <avr/io.h>
#include <util/delay.h>

int main (void)
{
    DDRB = 255; 
    while(1) 
    {
        PORTB ^= 255;
        _delay_ms(500);
    }
}

Here’s how I compiled the code:

avr-gcc -mmcu=atmega48 -Wall -Os -o blink.elf blink.c
avr-objcopy -j .text -j .data -O ihex blink.elf blink.hex

In reality, it is useful to put these commands in a text file and call them “compile.bat”

Here’s how I program the AVR. I used AVRDudess! I’ve been using raw AVRDude for years. It’s a little rough around the edges, but this GUI interface is pretty convenient. I don’t even feel the need to include the command to program it from the command line! If I encourage nothing else by this post, I encourage (a) people to use and support AVRDudess, and (b) AVRDudess to continue developing itself as a product nearly all hobby AVR programmers will use. Thank you 21-year-old Zak Kemble.

And finally, the result. A blinking LED. Up and running programming AVR microcontrollers in 64-bit Windows 7 with an unofficial programmer, and never needing to install bloated AVR Studio software.

Permanent link to this article: http://www.SWHarden.com/blog/2013-05-07-avr-programming-in-64-bit-windows-7/

Tenma 72-7750 Multimeter Excellent for RF Engineering

I recently got my hands on a Tenma 72-7750 multimeter. Tenma has a pretty large collection of test equipment and measurement products, including several varieties of hand-held multimeters. The 72-7750 multimeter has the standard measurement modes you’d expect (voltage, current capacitance, resistance, conductivity), but stood out to me because it also measures frequency, temperature, and has RS232 PC connectivity. Currently it’s sale from Newark for under fifty bucks! This is what mine arrived with:

The obvious stuff worked as expected. Auto ranging, (5 ranges of voltage and resistance, 3 of current, 7 of capacitance), accurate measurement, etc. I was, however, impressed with the extra set of test leads they provided – little short ones with gator clips! These are perfect for measuring capacitance, or for clipping onto wires coming out of a breadboard. So many times with my current multimeters I end-up gator-clipping wires to my probes and taking them to what I’m measuring. I’m already in love with the gator clip leads, and know I’ll have a set of these at my bench for the rest of my life.

I was impressed by the frequency measuring ability of this little multimeter! When I read that it could measure up to 60MHz, I was impressed, but also suspected it might be a little flakey. This was not at all the case – the frequency measurement was dead-on at several ranges! With so many of the projects I work on being RF-involved (radio transmitters, radio receivers, modulators, mixers, you name it), I sided with this meter because unlike some of its siblings this one is rated beyond 50Mz. I hooked it up to the frequency synthesizer I built based around an ad9850 direct digital synthesizer and played around. When the synthesizer was set to various frequencies, the multimeter followed it to the digit! Check out the pics of it in action, comparing the LCD screen frequency with that being displayed on the meter:

I also took a closer look at the PC interface. When I looked closely, I noticed it wasn’t an electrical connection – it was an optical one! It has a phototransistor on one end, and a serial connection on the other. I’m no stranger to tossing data around with light (I made something that did this here, which was later featured on Hack-A-Day here). I wondered what the format of the data was, when to my surprise I saw it spelled out in the product manual! (Go Tenma!)  It specifically says “Baud Rate 19230, Start Bit 1 (always 0), Stop bit 1 (always 1), Data bits (7), Parity 1 (odd)”. Although they have their own windows-only software to display/graph readings over time, I’d consider writing Python-based logging software. It should be trivial with python, pySerial, numpy, and matplotlib. Clearly I’m no stranger to graphing things in python :)

How does the photo-transistor work without power? I attached my o-scope to the pins and saw nothing when RS232 mode was activated on the multimeter. Presumably, the phototransistor requires a voltage source (albeit low current) to operate. With a little digging on the internet, I realized that the serial port can source power. I probably previously overlooked this because serial devices were a little before my time, but consider serial mice: they must have been supplied power! Joseph Sullivan has a cool write-up on a project which allowed him to achieve bidirectional optical (laser) communication over (and completely powered by) a serial port. With a little testing, I applied 0V to pin 5 (GND), +5V to pin 6 (DSR, data set ready), and looked at the output on pin 3 (PC RX). Sure enough, there were bursts of easy-to-decode RS232 data. Here’s the scheme Joseph came up with to power his laser communication system, which presumably is similar to the one in the multi-meter. (Note, that the cable is missing its “TX” light, but the meter has an “RX” phototransistor. I wonder if this would allow optically-loaded firmware?)

There were a couple other things I found useful. Although I didn’t appreciate it at first, after a few days the backlight grew on me. I’ve been doing experiments with photosensors which require me to turn out the lights in the room, and the backlight saved the day! Also, the meter came with a thermocouple for temperature measurement. It has it’s own “ºC” setting on the dial, and displays human-readable temperature right on the screen. I used to do this with LM334-type thermosensitive current sources but it was always a pain (especially if I had one which output temperature in Kelvin!) I’m not sure exactly what’s inside the one that came with this meter, but the datasheet suggests it can measure -40 through 1,000 C, which certainly will do for my experiments!

All in all, I’m happy with this little guy, and am looking forward to hacking into it a little bit. There may be enough room in the case to add a hacked-together high frequency divider (a decade counter would be fantastic, divided by ten would allow measurement through 500MHz), but I might be over-reaching a bit. Alternatively, a high gain preamplifier would be a neat way to allow the sort probe to serve as an antenna to measure frequency wirelessly, rater than requiring contact. Finally, I’m looking forward to writing software to interface the RS232 output. The ability to measure, record, and display changes in voltage or temperature over time is an important part of designing controller systems. For example, an improved crystal oven is on my list of projects to make. What a perfect way to monitor the temperature and stability of the completed project! Straight out of the box, this multimeter is an excellent tool.

Permanent link to this article: http://www.SWHarden.com/blog/2013-04-17-tenma-72-7750-multimeter-excellent-for-rf-engineering/

Fixing Slow Matplotlib in Python(x,y)

I recently migrated to Python(x,y) and noticed my matplotlib graphs are resizing unacceptably slowly when I use the pan/zoom button. I’m quite a fan of numpy, scipy, matplotlib, the python imaging library (PIL), and GUI platforms like Tk/TkInter, pyGTK, and pyQT, but getting them all to play nicely is a sometimes pain. I’m considering migrating entirely to Python(x,y) because, as a single distribution, it’s designed to install all these libraries (and many more) in a compatible way out of the box. However, when I did, I noticed matplotlib graphs would resize, rescale, and drag around the axes very slowly. After a lot of digging on the interweb, I figured out what was going wrong. I’ll show you by plotting 20 random data points the slow way (left) then the fast way (right).

THE PROBLEM: See the difference between the two plots? The one on the left (SLOW!) uses the Qt4Agg backend, which renders the matplotlib plot on a QT4 canvas. This is slower than the one on the right, which uses the more traditional TkAgg backend to draw the plot on a Tk canvas with tkinter (FASTER!). Check out matplotlib’s official description of what a backend is and which ones you can use. When you just install Python and matplotlib, Tk is used by default. 

import numpy
import matplotlib
matplotlib.use('TkAgg') # <-- THIS MAKES IT FAST!
import pylab
pylab.plot(numpy.random.random_integers(0,100,20))
pylab.title("USING: "+matplotlib.get_backend())
pylab.show()

THE FIX: Tell matplotlib to stop using QT to draw the plot, and let it plot with Tk. This can be done immediately after importing matplotlib, but must be done before importing pylab using the line matplotlib.use('TkAgg'). Here’s the full example I used to generate the demonstration plots above. Change TkAgg to Qt4Agg (or comment-out the ‘use’ line if you’re using PythonXY) and you will see performance go down the tube. Alternatively, make a change to the matplotlib rc file to customize default behavior when the package is loaded.

Permanent link to this article: http://www.SWHarden.com/blog/2013-04-15-fixing-slow-matplotlib-in-pythonxy/

Simple DIY ECG + Pulse Oximeter (version 2)

Of the hundreds of projects I’ve shared over the years, none has attracted more attention than my DIY ECG machine on the cheap posted almost 4 years ago. This weekend I re-visited the project and made something I’m excited to share!  The original project was immensely popular, my first featured article on Hack-A-Day, and today “ECG” still represents the second most searched term by people who land on my site. My gmail account also has had 194 incoming emails from people asking details about the project. A lot of it was by frustrated students trying to recreate the project running into trouble because it was somewhat poorly documented. Clearly, it’s a project that a wide range of people are interested in, and I’m happy to revisit it bringing new knowledge and insight to the project. I will do my best to document it thoroughly so anyone can recreate it!

The goal of this project is to collect heartbeat information on a computer with minimal cost and minimal complexity.  I accomplished this with fewer than a dozen components (all of which can be purchased at RadioShack). It serves both as a light-based heartbeat monitor (similar to a pulse oximeter, though it’s not designed to quantitatively measure blood oxygen saturation), and an electrocardiogram (ECG) to visualize electrical activity generated by heart while it contracts. Let’s jump right to the good part – this is what comes out of the machine:

That’s my actual heartbeat. Cool, right? Before I go into how the circuit works, let’s touch on how we measure heartbeat with ECG vs. light (like a pulse oximeter).  To form a heartbeat, the pacemaker region of the heart (called the SA node, which is near the upper right of the heart) begins to fire and the atria (the two top chambers of the heart) contract. The SA node generates a little electrical shock which stimulated a synchronized contraction. This is exactly what defibrillators do when a heart has stopped beating. When a heart attack is occurring and a patient is undergoing ventricular fibrillation, it means that heart muscle cells are contracting randomly and not in unison, so the heart quivers instead of pumping as an organ. Defibrillators synchronize the heart beat with a sudden rush of current over the heart to reset all of the cells to begin firing at the same time (thanks Ron for requesting a more technical description).  If a current is run over the muscle, the cells (cardiomyocytes) all contract at the same time, and blood moves. The AV node (closer to the center of the heart) in combination with a slow conducting pathway (called the bundle of His) control contraction of the ventricles (the really large chambers at the bottom of the heart), which produce the really large spikes we see on an ECG.  To measure ECG, optimally we’d place electrodes on the surface of the heart. Since that would be painful, we do the best we can by measuring voltage changes (often in the mV range) on the surface of the skin. If we amplify it enough, we can visualize it. Depending on where the pads are placed, we can see different regions of the heart contract by their unique electrophysiological signature. ECG requires sticky pads on your chest and is extremely sensitive to small fluctuations in voltage. Alternatively, a pulse oximeter measures blood oxygenation and can monitor heartbeat by clipping onto a finger tip. It does this by shining light through your finger and measuring how much light is absorbed. This goes up and down as blood is pumped through your finger. If you look at the relationship between absorbency in the red vs. infrared wavelengths, you can infer the oxygenation state of the blood. I’m not doing that today because I’m mostly interested in detecting heart beats.

For operation as a pulse oximeter-type optical heartbeat detector (a photoplethysmograph which produces a photoplethysmogram), I use a bright red LED to shine light through my finger and be detected by a phototransistor (bottom left of the diagram). I talk about how this works in more detail in a previous post. Basically the phototransistor acts like a variable resistor which conducts different amounts of current depending on how much light it sees. This changes the voltage above it in a way that changes with heartbeats. If this small signal is used as the input, this device acts like a pulse oximeter.

For operation as an electrocardiograph (ECG), I attach the (in) directly to a lead on my chest. One of them is grounded (it doesn’t matter which for this circuit – if they’re switched the ECG just looks upside down), and the other is recording. In my original article, I used pennies with wires soldered to them taped to my chest as leads. Today, I’m using fancier sticky pads which are a little more conductive. In either case, one lead goes in the center of your chest, and the other goes to your left side under your arm pit. I like these sticky pads because they stick to my skin better than pennies taped on with electrical tape. I got 100 Nikomed Nikotabs EKG Electrodes 0315 on eBay for $5.51 with free shipping (score!). Just gator clip to them and you’re good to go!

In both cases, I need to build a device to amplify small signals. This is accomplished with the following circuit. The core of the circuit is an LM324 quad operational amplifier.  These chips are everywhere, and extremely cheap. It looks like Thai Shine sells 10 for $2.86 (with free shipping). That’s about a quarter each. Nice!  A lot of ECG projects use instrumentation amplifiers like the AD620 (which I have used with fantastic results), but these are expensive (about $5.00 each). The main difference is that instrumentation amplifiers amplify the difference between two points (which reduces noise and probably makes for a better ECG machine), but for today an operational amplifier will do a good enough job amplifying a small signal with respect to ground. I get around the noise issue by some simple filtering techniques. Let’s take a look at the circuit.

This project utilizes one of the op-amps as a virtual ground. One complaint of using op-amps in simple projects is that they often need + and – voltages. Yeah, this could be done with two 9V batteries to generate +9V and -9V, but I think it’s easier to use a single power source (+ and GND). A way to get around that is to use one of the op-amps as a current source and feed it half of the power supply voltage (VCC), and use the output as a virtual ground (allowing VCC to be your + and 0V GND to be your -). For a good description of how to do this intelligently, read the single supply op amps web page. The caveat is that your signals should remain around VCC/2, which can be done if it is decoupled by feeding it through a series capacitor. The project works at 12V or 5V, but was designed for (and has much better output) at 12V. The remaining 3 op-amps of the LM324 serve three unique functions:

STAGE 1: High gain amplifier. The input signals from either the ECG or pulse oximeter are fed into a chain of 3 opamp stages. The first is a preamplifier. The output is decoupled through a series capacitor to place it near VCC/2, and amplified greatly thanks to the 1.8Mohm negative feedback resistor. Changing this value changes initial gain.

STAGE 2: active low-pass filter. The 10kOhm variable resistor lets you adjust the frequency cutoff. The opamp serves as a unity gain current source / voltage follower that has high input impedance when measuring the output f the low-pass filter and reproduces its voltage with a low impedance output. There’s some more information about active filtering on this page. It’s best to look at the output of this stage and adjust the potentiometer until the 60Hz noise (caused by the AC wiring in the walls) is most reduced while the lower-frequency component of your heartbeat is retained. With the oximeter, virtually no noise gets through. Because the ECG signal is much smaller, this filter has to be less aggressive, and this noise is filtered-out by software (more on this later).

STAGE 3: final amplifier with low-pass filter. It has a gain of ~20 (determined by the ratio of the 1.8kOhm to 100Ohm resistors) and lowpass filtering components are provided by the 22uF capacitor across the negative feedback resistor. If you try to run this circuit at 5V and want more gain (more voltage swing), consider increasing the value of the 1.8kOhm resistor (wit the capacitor removed). Once you have a good gain, add different capacitor values until your signal is left but the noise reduced. For 12V, these values work fine. Let’s see it in action!

Now for the second half – getting it into the computer. The cheapest and easiest way to do this is to simply feed the output into a sound card! A sound card is an analog-to-digital converter (ADC) that everybody has and can sample up to 48 thousand samples a second! (overkill for this application) The first thing you should do is add an output potentiometer to allow you to drop the voltage down if it’s too big for the sound card (in the case of the oximeter) but but also allow full-volume in the case of sensitive measurements (like ECG). Then open-up sound editing software (I like GoldWave for Windows or Audacity for Linux, both of which are free) and record the input. You can do filtering (low-pass filter at 40Hz with a sharp cutoff) to further eliminate any noise that may have sneaked through. Re-sample at 1,000 Hz (1kHz) and save the output as a text file and you’re ready to graph it! Check it out.

Here are the results of some actual data recorded and processed with the method shown in the video. let’s look at the pulse oximeter first.

That looks pretty good, certainly enough for heartbeat detection. There’s obvious room for improvement, but as a proof of concept it’s clearly working. Let’s switch gears and look at the ECG. It’s much more challenging because it’s signal is a couple orders of magnitude smaller than the pulse oximeter, so a lot more noise gets through. Filtering it out offers dramatic improvements!

Here’s the code I used to generate the graphs from the text files that GoldWave saves. It requires Python, Matplotlib (pylab), and Numpy. In my case, I’m using 32-bit 2.6 versions of everything.

# DIY Sound Card ECG/Pulse Oximeter
# by Scott Harden (2013) http://www.SWHarden.com

import pylab
import numpy

f=open("light.txt")
raw=f.readlines()[1:]
f.close()

data = numpy.array(raw,dtype=float)
data = data-min(data) #make all points positive
data = data/max(data)*100.0 #normalize
times = numpy.array(range(len(data)))/1000.0
pylab.figure(figsize=(15,5))
pylab.plot(times,data)
pylab.xlabel("Time Elapsed (seconds)")
pylab.ylabel("Amplitude (% max)")
pylab.title("Pulse Oximeter - filtered")
pylab.subplots_adjust(left=.05,right=.98)
pylab.show()

Future directions involve several projects I hope to work on soon. First, it would be cool to miniaturize everything with surface mount technology (SMT) to bring these things down to the size of a postage stamp. Second, improved finger, toe, or ear clips (or even taped-on sensors) over long duration would provide a pretty interesting way to analyze heart rate variability or modulation in response to stress, sleep apnea, etc. Instead of feeding the signal into a computer, one could send it to a micro-controller for processing. I’ve made some darn-good progress making multi-channel cross-platform USB option for getting physiology data into a computer, but have some work still to do. Alternatively, this data could be graphed on a graphical LCD for an all-in-one little device that doesn’t require a computer. Yep, lots of possible projects can use this as a starting point.

Notes about safety: If you’re worried about electrical shock, or unsure of your ability to make a safe device, don’t attempt to build an ECG machine. For an ECG to work, you have to make good electrical contact with your skin near your heart, and some people feel this is potentially dangerous. Actually, some people like to argue about how dangerous it actually is, as seen on Hack-A-Day comments and my previous post comments. Some people have suggested the danger is negligible and pointed-out that it’s similar to inserting ear-bud headphones into your ears. Others have suggested that it’s dangerous and pointed-out that milliamps can kill a person. Others contest that pulses of current are far more dangerous than a continuous applied current. Realists speculate that virtually no current would be delivered by this circuit if it is wired properly. Rational, cautionary people worried about it reduce risk of accidental current by applying bidirectional diodes at the level of the chest leads, which short any current (above 0.7V) similar to that shown here. Electrically-savvy folks would design an optically decoupled solution. Intelligent folks who abstain from arguing on the internet would probably consult the datasheets regarding ECG input protection. In all cases, don’t attach electrical devices to your body unless you are confident in their safety. As a catch-all, I present the ECG circuit for educational purposes only, and state that it may not be safe and should not be replicated  There, will that cover me in court in case someone tapes wires to their chest and plugs them in the wall socket?

LET ME KNOW WHAT YOU THINK! If you make this, I’m especially interested to see how it came out. Take pictures of your projects and send them my way! If you make improvements, or take this project further, I’d be happy to link to it on this page. I hope this page describes the project well enough that anyone can recreate it, regardless of electronics experience. Finally, I hope that people are inspired by the cool things that can be done with surprisingly simple electronics. Get out there, be creative, and go build something cool!

Permanent link to this article: http://www.SWHarden.com/blog/2013-04-14-simple-diy-ecg-pulse-oximeter-version-2/

AVR Programming in Linux

It is not difficult to program ATMEL AVR microcontrollers with linux, and I almost exclusively do this because various unofficial (inexpensive) USB AVR programmers are incompatible with modern versions of windows (namely Windows Vista and Windows 7). I am just now setting-up a new computer station in my electronics room (running Ubuntu Linux 12.04), and to make it easy for myself in the future I will document everything I do when I set-up a Linux computer to program microcontrollers.

Install necessary software

sudo apt-get install gcc-avr avr-libc uisp avrdude

Connect the AVR programmer
This should be intuitive for anyone who has programmed AVRs before. Visit the datasheet of your MCU, identify pins for VCC (+), GND (-), MOSI, MISO, SCK, and RESET, then connect them to the appropriate pins of your programmer.

Write a simple program in C
I made a file “main.c” and put the following inside. It’s the simplest-case code necessary to make every pin on PORTD (PD0, PD1, …, PD7) turn on and off repeatedly, sufficient to blink an LED.

#include <avr/io.h>
#include <util/delay.h>

int main (void)
{
 DDRD = 255; // MAKE ALL PORT D PINS OUTPUTS

 while(1) {
  PORTD = 255;_delay_ms(100); // LED ON
  PORTD = 0;  _delay_ms(100); // LED OFF
 }

 return 0;
}

Compile the code (generate a HEX file)

avr-gcc -w -Os -DF_CPU=2000000UL -mmcu=atmega8 -c -o main.o main.c
avr-gcc -w -mmcu=atmega8 main.o -o main
avr-objcopy -O ihex -R .eeprom main main.hex

note that the arguments define CPU speed and chip model – this will need to be customized for your application

Program the HEX firmware onto the AVR

sudo avrdude -F -V -c avrispmkII -p ATmega8 -P usb -U flash:w:main.hex

note that this line us customized based on my connection (-P flag, USB in my case) and programmer type (-c flag, AVR ISP mkII in my case)

When this is run, you will see something like this:


avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.01s

avrdude: Device signature = 0x1e9307
avrdude: NOTE: FLASH memory has been specified, an erase cycle will be performed
         To disable this feature, specify the -D option.
avrdude: erasing chip
avrdude: reading input file "main.hex"
avrdude: input file main.hex auto detected as Intel Hex
avrdude: writing flash (94 bytes):

Writing | ################################################## | 100% 0.04s

avrdude: 94 bytes of flash written

Your Program should now be loaded! Sit back and watch your LED blink.

TIP 1: I’m using a clone AVRISP mkII from Fun4DIY.com which is only $11 (shipped!). I glued it to a perf-board with a socket so I can jumper its control pins to any DIP AVR (80 pins or less). I also glued a breadboard for my convenience, and added LEDs (with ground on one of their pins) for easy jumpering to test programs. You can also build your own USB AVR ISP (free schematics and source code) from the USBtinyISP project website.

TIP 2: Make a shell script to run your compiling / flashing commands with a single command. Name them according to architecture. i.e., “build-m8″ or “build-t2313″. Make the first line delete all .hex files in the directory, so it stalls before it loads old .hex files if the compile is unsuccessful. Make similar shell scripts to program fuses. i.e., “fuse-m8-IntClock-8mhz”, “fuse-m8-IntClock-1mhz”, “fuse-m8-ExtCrystal”.

TIP 3: Use a nice text editor well suited for programming. I love Geany.

Permanent link to this article: http://www.SWHarden.com/blog/2013-01-06-avr-programming-in-linux/

My DIY Bench Power Supply

Another thing everybody needs (and has probably built) is a simple laboratory bench power supply. A lot of people use things like modified PC power supplies but I wasn’t in favor of this because I wanted something smaller, lower current, and cleaner (from an RF perspective). My needs are nothing particularly high power, just something to provide a few common voltages for digital logic and small RF circuits. This is what I came up with!

In the image above you can see an ordinary LED being powered directly from the a 5V hook-up. There is no current limiting resistor, so a lot of current is travelling through the LED, burning it up as I photographed it. The ammeter (blue number) shows it’s drawing 410 mA – whoa! The layout is pretty simple. Each red banana plug hook-up supplies a voltage (5, 5, 12, and variable respectively). Black hook-ups are ground. The black hook-up on the top left is a current-sensing ground, and current travelling through it will be displayed on the blue dial. The right dial shows the voltage of the variable voltage supply, and can go from about 3.5 – 30.5 V depending on where the potentiometer is set. All voltage outputs are designed to put-out approximately 1A of current.

I built this using a lot of (eBay) components I had on hand. I often save money where I can by stocking my workbench with components I buy in bulk. Here’s what I used:

  • 4.5-3.0V DC volt meter – $2.08 (shipped) eBay
  • 0-9.99 A ampere meter – $4.44 (shipped) eBay
  • L7805 5V voltage regulator – 10 for $3.51 ($.35 ea) (shipped) eBay
  • L7812 12V voltage regulator – 20 for $3.87 ($.19 ea) (shipped) eBay
  • LM317 variable voltage regulator – 20 for $6.15 ($0.30 ea) (shipped) eBay
  • 10k linear potentiometer – 10 for 4.00 ($.40 ea) (shipped) eBay
  • banana plug hook-ups – 20 for $3.98 ($.20 ea) (shipped) eBay
  • aluminum enclosure – $3.49 (radioshack)

TOTAL: $13.60

Does the variable voltage actually work? Is the voltmeter accurate? Let’s check it out.

I’d say it’s working nicely! I now have a new took on my workbench.

A note about the yellow color: The enclosure I got was originally silver aluminum. I sanded it (to roughen the surface), then sprayed it with a yellow rustoleum spray paint. I figured it was intended to go on metal, so I might as well give it a shot. I sprayed it once, then gave it a second coat 20 minutes later, then let it dry overnight. In the future I think I would try a lacquer finish, because it’s a bit easy to scratch off. However, it looks pretty cool, and I’m going to have to start spray-painting more of my enclosures in the future.

A note about smoothing capacitors. Virtually all diagrams of linear voltage regulators like the LM7805 show decoupling capacitors before and after the regulator. I added a few different values of capacitors on the input (you can see them in the circuit), but I intentionally did not include smoothing capacitors on the output. The reason was that I always put smoothing capacitors in my breadboards and in my projects, closer to the actual circuitry. If I included (and relied) on output capacitors at the level of the power supply, I would be picking-up 60Hz (and other garbage) RF noise in the cables coming from the power supply to my board. In short, no capacitors on the output, so good design must always be employed and decoupling capacitors added to whatever circuits are being built.

The input of this circuit is a 48V printer power supply from an archaic inkjet printer. It’s been attached to an RCA jack to allow easy plugging and unplugging.

Permanent link to this article: http://www.SWHarden.com/blog/2012-12-18-my-diy-bench-power-supply/

Single Wavelength Pulse Oximeter

I want to create a microcontroller application which will utilize information obtained from a home-brew pulse oximeter. Everybody and their cousin seems to have their own slant how to make DIY pulse detectors, but I might as well share my experience. Traditionally, pulse oximeters calculate blood oxygen saturation by comparing absorbance of blood to different wavelengths of light. In the graph below (from Dildy et al., 1996 that deoxygenated blood (dark line) absorbs light differently than oxygenated blood (thin line), especially at 660nm (red) and 920nm (infrared). Therefore, the ratio of the difference of absorption at 660nm vs 920nm is an indication of blood oxygenation. Fancy (or at least well-designed) pulse oximeters continuously look at the ratio of these two wavelengths. Analog devices has a nice pulse oximeter design using an ADuC7024 microconverter. A more hackerish version was made and described on this non-english forum. A fail-at-the-end page of a simpler project is also shown here, but not well documented IMO.

That’s not how mine works. I only use a single illumination source (~660nm) and watch it change with respect to time. Variability is due to a recombination effect of blood volume changes and blood oxygen saturation changes as blood pulses through my finger. Although it’s not quite as good, it’s a bit simpler, and it definitely works. Embedded-lab has a similar project but the output is only a pulsing LED (not what I want) and a voltage output that only varies by a few mV (not what I want).

Here’s what the device looks like assembled in a breadboard:

I made a sensor by drilling appropriately-sized holes in a clothespin for the emitter (LED) and sensor (phototransistor). I had to bend the metal spring to make it more comfortable to wear. Light pressure is better than firm pressure, not only because it doesn’t hurt as much, but because a firm pinch restricts blood flow considerably.

An obvious next step is microcontroller + LCD (or computer) digitization, but for now all you can do is check it out on my old-school analog oscilloscope. Vertical squares represent 1V (nice!). You can see the pulse provides a solid 2V spike.

Here’s some video of it in action:

Out of principal, I’m holding-back the circuit diagram until I work through it a little more. I don’t want to mislead people by having them re-create ill-conceived ideas on how to create analog amplifiers. I’ll post more as I develop it.

Permanent link to this article: http://www.SWHarden.com/blog/2012-12-06-single-wavelength-pulse-oximeter/

Geek Spin – ATTiny44 Project Prototype

Some days you feel like working on projects to benefit humanity. The day I made this clearly wasn’t one of those days. A little over a year ago, I got into a troll war with my friend Mike Seese. The joke, similar to that of rick rolling, was to get each other to unexpectedly click a link to the Hatsune Miku version of the leekspin song. After several weeks of becoming beyond annoying, I decided to make an actual Hatsune Miku which would spin her leek and bobble her head to the techno version of the Levan Polka for his birthday.

The goal was to create a minature Miku which would perform perfectly in sync with audio coming from a portable music player (iPod or something) and NOT require a computer connection. I accomplished it by sending some creative control beeps out of the left channel of the stereo signal. Although I didn’t finish the project, I got pretty far with the prototype, so I decided to dig it out of the archives and share it with the world because it’s pretty entertaining!


(look how close I came to replicating the original!)

How did I do it? First off, I used servos. If you’re not familiar with them, I suggest you look up how servos work. Perhaps check out how to control servos with AVR microcontrollers. Basically, their position along a rotational axis is determined by the width of a pulse on a 20ms time window. Anyhow, if I only had 1 servo to control (i.e., leek only), I’d have controlled the servo directly with PWM signals in the left channel – no microcontroller needed, easy as pie, problem solved. However, since I needed to control two servos, I had to come up with something a bit more creative. Although I could have probably done this ten different ways, the way I chose to do it was using a series of pre-encoded leek spin and head bobble motions, triggered by control beeps in the left channel of the audio cable. (The right channel was patched through to the speakers.) Below is a diagram of what I believe I did, although I didn’t thoroughly document it at the time, so you might have to use your imagination if you decide to re-create this project.

The idea is that by sending bursts of sine waves, the circuit can rectify them and smooth them out to have them look to a microcontroller like a brief “high” signal. Each signal would tell the microcontroller to proceed to the next pre-programmed (and carefully timed) routine. With enough practice listening, watching, and tweaking the code, I was able to make a final version which worked pretty darn well!

LISTEN TO:MUSIC WITH CONTROL BEEPS (it’s a surprisingly fun listen)

A few technical details are that I used an ATTiny44a microcontroller (it may have been an ATTiny2313, I can’t remember for sure, but they’re so similar it’s virtually negligable). The servos I used were cheap (maybe $4?) from eBay. They looked like the one pictured below. The servo position was controlled by PWM, but I manually sent the pulses and didn’t actually use the integrated PWM in the microcontroller. I can’t remember why I did it this way – perhaps because it was so simple to use the _delay_us() and _delay_ms() functions? I also used an operational amplifier (if I remember, it was a LM741) to boost the left channel control signals rather than rectifying/assessing the left channel directly.

This is the video which I mimiced to create my prototype (note how the leek in her arm and her head move exactly the same as the prototype I made – score!)

For good measure, here’s the original song:

And how did I find out about this song? I actually saw it on the video below which was hosted on wimp.com. I thought the song was catchy, looked it up, and the rest was history. It’s worth noting that (perhaps to avoid copyright issues?) the key was shifted two half-steps up. I get a kick out of the way the girl waves her arm in the beginning, mimicking the leek :)

Here are some of the images I made which I printed, glued to foam board, and cut out with a razor blade. I’m not sure how useful they are, but they’re provided just in case.


… but sometimes Japan takes it a bit too far and things get awkward …

Below is the code I used. Note that PWM that controls the servos isn’t the integrated PWM, but rather a couple pins I manually pulse on and off to control the arm and head positions. Also notice how, in the main routine, I wait for the control beeps before continuing the next sequences.

// leek spin code - designed for ATTiny
// by Scott Harden, www.SWHarden.com

#include <avr/io.h>
#include <avr/delay.h>

void go_high(){
	// sets the arm to the highest position
	for (char i=0;i<5;i++){
		PORTA|=(1<<PA0);
		_delay_us(1400);
		PORTA&=~(1<<PA0);
		_delay_us(20000-1200);
		}
	}
		
void go_low(){
	// sets the leek to the middle position
	for (char i=0;i<5;i++){
		PORTA|=(1<<PA0);
		_delay_us(1900);
		PORTA&=~(1<<PA0);
		_delay_us(20000-1900);
		}
	}
		
void go_lowest(){
	// sets the leek to the lowest position
	for (char i=0;i<5;i++){ // takes 100ms total
		PORTA|=(1<<PA0);
		_delay_us(2300);
		PORTA&=~(1<<PA0);
		_delay_us(20000-2500);
		}
	}

void go_slow(char times){
	// does one slow leek down/up
	// beat is 500ms
	for (char i=0;i<times;i++){
		go_low();
		_delay_ms(10);
		go_high();
		_delay_ms(290);
		PORTA^=(1<<PA2);
		PORTA^=(1<<PA3);
	}
}

void go_fast(char times){
	// does one fast leek down/up
	// beat is 250ms
	for (char i=0;i<times;i++){
		go_low();
		_delay_ms(10);
		go_high();
		_delay_ms(15);
		PORTA^=(1<<PA2);
		PORTA^=(1<<PA3);
	}
}
void head_left(){
	// tilts the head to the left
	for (char i=0;i<5;i++){
		PORTA|=(1<<PA1);
		_delay_us(1330);
		PORTA&=~(1<<PA1);
		_delay_us(20000-1200);
		}
	}

void head_right(){
	// tilts the head to the right
	for (char i=0;i<5;i++){
		PORTA|=(1<<PA1);
		_delay_us(1500);
		PORTA&=~(1<<PA1);
		_delay_us(20000-1200);
		}
	}

void head_center(){
	// centers the head
	for (char i=0;i<5;i++){
		PORTA|=(1<<PA1);
		_delay_us(1400);
		PORTA&=~(1<<PA1);
		_delay_us(20000-1200);
		}
	}

void head_go(char times){
	// rocks the head back and forth once
	for (char i=0;i<(times-1);i++){
		head_left();
		_delay_ms(400);
		PORTA^=(1<<PA2);
		PORTA^=(1<<PA3);
		head_right();
		_delay_ms(400);
		PORTA^=(1<<PA2);
		PORTA^=(1<<PA3);
	}
	head_center(); // returns head to center when done
	_delay_ms(400);
	PORTA^=(1<<PA2);
	PORTA^=(1<<PA3);
}

int main(void) {
	while (1){
		DDRA=255; // set port A (servos) as outputs
		DDRB=0; // set port B (listening pins) as inputs
		
		go_lowest();head_center();// set starting positions

		while ((PINB & _BV(PB0))){} // wait for beep que
		PORTA=(1<<PA3);
		go_high();_delay_ms(1000);
		while ((PINB & _BV(PB0))){} // wait for beep que
		go_slow(31); // tilt leek slowly 31 times
		while ((PINB & _BV(PB0))){} // wait for beep que
		go_slow(31); // tilt leek slowly 31 times
		
		while ((PINB & _BV(PB0))){} // wait for beep que
		_delay_ms(200);
		head_go(16); // rock head 16 times
		while ((PINB & _BV(PB0))){} // wait for beep que
		go_fast(68); // tilt leek rapidly 68 times
		while ((PINB & _BV(PB0))){} // wait for beep que
		go_slow(24); // tilt leek slowly 24 times
		while ((PINB & _BV(PB0))){} // wait for beep que
		go_fast(17); // tilt leek rapidly 17 times
		while ((PINB & _BV(PB0))){} // wait for beep que
		go_slow(31); // tilt leek slowly 31 times
		while ((PINB & _BV(PB0))){} // wait for beep que
		go_slow(31); // tilt leek slowly 31 times
		
		while ((PINB & _BV(PB0))){} // wait for beep que
		_delay_ms(200);
		head_go(16); // rock head 16 times
		go_lowest(); // reset position
		PORTA=0;
	}
  return 0;
}

Finally, I’d like to take a moment to indicate one of the reasons this project is special to me. My wife, Angelina Harden, died one year ago today. This project was the last one she worked on with me. She died a few days after the video was taken, and in the process of moving out of our apartment I threw away almost everything (including this project). Although I never finished it, I remember working on it with Angelina – we went to wal-mart together to buy the foam board I used to make it, and she told me that I should make her head rock back and forth rather than just move her arm. I remember that, once it was all done, I let her sit in the chair in front of it and played it through, and she laughed nearly the whole time :) I’ll always miss her.

Permanent link to this article: http://www.SWHarden.com/blog/2012-08-18-geek-spin-attiny44-project-prototype/

Introduction to PIC Programming from an AVR Guru

I’m not ashamed to say it: I’m a bit of an ATMEL guy. AVR microcontrollers are virtually exclusively what I utilize when creating hobby-level projects. Wile I’d like to claim to be an expert in the field since I live and breathe ATMEL datasheets and have used many intricate features of these microchips, the reality is that I have little experience with other platforms, and have likely been leaning on AVR out of habit and personal convention rather than a tangible reason. Although I was initially drawn to the AVR line of microcontrollers because of its open-source nature (The primary compiler is the free AVR-GCC) and longstanding ability to be programmed from non-Windows operating systems (like Linux), Microchip’s PIC has caught my eye over the years because it’s often a few cents cheaper, has considerably large professional documentation, and offers advanced integrated peripherals (such as native USB functionality in a DIP package) more so than the current line of ATTiny and ATMega microcontrollers. From a hobby standpoint, I know that ATMEL is popular (think Arduino), but from a professional standpoint I usually hear about commercial products utilizing PIC microcontrollers. One potential drawback to PIC (and the primary reason I stayed away from it) is that full-featured C compilers are often not free, and as a student in the medical field learning electrical engineering as a hobby, I’m simply not willing to pay for software at this stage in my life.

I decided to take the plunge and start gaining some experience with the PIC platform. I ordered some PIC chips (a couple bucks a piece), a PIC programmer (a Chinese knock-off clone of the Pic Kit 2 which is <$20 shipped on eBay), and shelved it for over a year before I got around to figuring it out today. My ultimate goal is to utilize its native USB functionality (something at ATMEL doesn’t currently offer in DIP packages). I’ve previously used bit-banging libraries like V-USB to hack together a USB interface on AVR microcontrollers, but it felt unnecessarily complex. PIC is commonly used and a bit of an industry standard, so I’m doing myself a disservice by not exploring it. My goal is USB functionality, but I have to start somewhere: blinking a LED.

Here’s my blinking LED. It’s a bit anticlimactic, but it represents a successful program design from circuit to writing the code to programming the microchip.

Based on my limited experience, it seems you need 4 things to program a PIC microcontroller with C:

The first thing I did was familiarize myself with the pin diagram of my PIC from its datasheet. I’m playing with an 18F2450 and the datasheet is quite complete. If you look at the pin diagram, you can find pins labeled MCLR (reset), VDD (+5V), VSS (GND), PGC (clock), and PGD (data). These pins should be connected to their respective counterparts on the programmer. To test connectivity, install and run the PICkit2 installer software and it will let you read/verify the firmware on the chip, letting you know connectivity is solid. Once you’re there, you’re ready to start coding!

I wish I were friends with someone who programmed PIC, such that in 5 minutes I could be shown what took a couple hours to figure out. There are quite a few tutorials out there – borderline too many, and they all seem to be a bit different. To quickly get acquainted with the PIC programming environment, I followed the “Hello World” Program in C tutorial on PIC18F.com. Unfortunately, it didn’t work as posted, likely because their example code was based on a PIC 18F4550 and mine is an 18F2450, but I still don’t understand why such a small difference caused such a big problem. The problem was in their use of LATDbits and TRISDbits (which I tried to replace with LATBbits and TRISBbits). I got around it by manually addressing TRISB and LATB. Anyway, this is what I came up with:

#include <p18f2450.h> // load pin names
#include <delays.h>   // load delay library

#pragma config WDT = OFF // disable watchdog timer
#pragma config FOSC = INTOSCIO_EC // use internal clock

void main() // this is the main program
{
	TRISB=0B00000000; // set all pins on port B as output
	while(1) // execute the following code block forever
	{
		LATB = 0b11111111; // turn all port B pins ON
		Delay10KTCYx(1);   // pause 1 second
		LATB = 0b00000000; // turn all port B pins OFF
		Delay10KTCYx(1);   // pause 1 second
	}
}


A couple notes about the code: the WDT=OFF disables the watchdog timer, which if left unchecked would continuously reboot the microcontroller. The FOSC=INTOSCIO_EC section tells the microcontroller to use its internal oscillator, allowing it to execute code without necessitating an external crystal or other clock source. As to what TRIS and LAT do, I’ll refer you to basic I/O operations with PIC.

Here is what the MPLAB IDE looked like after I successfully loaded the code onto the microcontroller. At this time, the LED began blinking about once per second. I guess that about wraps it up! This afternoon I pulled a PIC out of my junk box and, having never programmed a PIC before, successfully loaded the software, got my programmer up and running, and have a little functioning circuit. I know it isn’t that big of a deal, but it’s a step in the right direction, and I’m glad I’ve taken it.

Permanent link to this article: http://www.SWHarden.com/blog/2012-06-24-introduction-to-pic-programming-from-an-avr-guru/

Multichannel USB Analog Sensor with ATMega48

Sometimes it’s tempting to re-invent the wheel to make a device function exactly the way you want. I am re-visiting the field of homemade electrophysiology equipment, and although I’ve already published a home made electocardiograph (ECG), I wish to revisit that project and make it much more elegant, while also planning for a pulse oximeter, an electroencephalograph (EEG), and an electrogastrogram (EGG). This project is divided into 3 major components: the low-noise microvoltage amplifier, a digital analog to digital converter with PC connectivity, and software to display and analyze the traces. My first challenge is to create that middle step, a device to read voltage (from 0-5V) and send this data to a computer.

This project demonstrates a simple solution for the frustrating problem of sending data from a microcontroller to a PC with a USB connection. My solution utilizes a USB FTDI serial-to-usb cable, allowing me to simply put header pins on my device which I can plug into providing the microcontroller-computer link. This avoids the need for soldering surface-mount FTDI chips (which gets expensive if you put one in every project). FTDI cables are inexpensive (about $11 shipped on eBay) and I’ve gotten a lot of mileage out of mine and know I will continue to use it for future projects. If you are interested in MCU/PC communication, consider one of these cables as a rapid development prototyping tool. I’m certainly enjoying mine!

It is important to me that my design is minimalistic, inexpensive, and functions natively on Linux and Windows without installing special driver-related software, and can be visualized in real-time using native Python libraries, such that the same code can be executed identically on all operating systems with minimal computer-side configuration. I’d say I succeeded in this effort, and while the project could use some small touches to polish it up, it’s already solid and proven in its usefulness and functionality.

This is my final device. It’s reading voltage on a single pin, sending this data to a computer through a USB connection, and custom software (written entirely in Python, designed to be a cross-platform solution) displays the signal in real time. Although it’s capable of recording and displaying 5 channels at the same time, it’s demonstrated displaying only one. Let’s check-out a video of it in action:

This 5-channel realtime USB analog sensor, coupled with custom cross-platform open-source software, will serve as the foundation for a slew of electrophysiological experiments, but can also be easily expanded to serve as an inexpensive multichannel digital oscilloscope. While more advanced solutions exist, this has the advantage of being minimally complex (consisting of a single microchip), inexpensive, and easy to build.

 To the right is my working environment during the development of this project. You can see electronics, my computer, microchips, and coffee, but an intriguingly odd array of immunological posters in the background. I spent a couple weeks camping-out in a molecular biology laboratory here at UF and got a lot of work done, part of which involved diving into electronics again. At the time this photo was taken, I hadn’t worked much at my home workstation. It’s a cool picture, so I’m holding onto it.

Below is a simplified description of the circuit schematic that is employed in this project. Note that there are 6 ADC (analog to digital converter) inputs on the ATMega48 IC, but for whatever reason I ended-up only hard-coding 5 into the software. Eventually I’ll go back and re-declare this project a 6-channel sensor, but since I don’t have six things to measure at the moment I’m fine keeping it the way it is. RST, SCK, MISO, and MOSI are used to program the microcontroller and do not need to be connected to anything for operation. The max232 was initially used as a level converter to allow the micro-controller to communicate with a PC via the serial port. However, shortly after this project was devised an upgrade was used to allow it to connect via USB. Continue reading for details…

Below you can see the circuit breadboarded. The potentiometer (small blue box) simulated an analog input signal.

The lower board is my AVR programmer, and is connected to RST, SCK, MISO, MOSI, and GND to allow me to write code on my laptop and program the board. It’s a Fun4DIY.com AVR programmer which can be yours for $11 shipped! I’m not affiliated with their company, but I love that little board. It’s a clone of the AVR ISP MK-II.

As you can see, the USB AVR programmer I’m using is supported in Linux. I did all of my development in Ubuntu Linux, writing AVR-GCC (C) code in my favorite Linux code editor Geany, then loaded the code onto the chip with AVRDude.

I found a simple way to add USB functionality in a standard, reproducible way that works without requiring the soldering of a SMT FTDI chip, and avoids custom libraries like V-USB which don’t easily have drivers that are supported by major operating systems (Windows) without special software. I understand that the simplest long-term and commercially-logical solution would be to use that SMT chip, but I didn’t feel like dealing with it. Instead, I added header pins which allow me to snap-on a pre-made FTDI USB cable. They’re a bit expensive ($12 on ebay) but all I need is 1 and I can use it in all my projects since it’s a sinch to connect and disconnect. Beside, it supplies power to the target board! It’s supported in Linux and in Windows with established drivers that are shipped with the operating system. It’s a bit of a shortcut, but I like this solution. It also eliminates the need for the max232 chip, since it can sense the voltages outputted by the microcontroller directly.

The system works by individually reading the 10-bit ADC pins on the microcontroller (providing values from 0-1024 to represent voltage from 0-5V or 0-1.1V depending on how the code is written), converting these values to text, and sending them as a string via the serial protocol. The FTDI cable reads these values and transmits them to the PC through a USB connection, which looks like “COM5″ on my Windows computer. Values can be seen in any serial terminal program (i.e., hyperterminal), or accessed through Python with the PySerial module.

As you can see, I’m getting quite good at home-brewn PCBs. While it would be fantastic to design a board and have it made professionally, this is expensive and takes some time. In my case, I only have a few hours here or there to work on projects. If I have time to design a board, I want it made immediately! I can make this start to finish in about an hour. I use a classic toner transfer method with ferric chloride, and a dremel drill press to create the holes. I haven’t attacked single-layer SMT designs yet, but I can see its convenience, and look forward to giving it a shot before too long.

Here’s the final board ready for digitally reporting analog voltages. You can see 3 small headers on the far left and 2 at the top of the chip. These are for RST, SCK, MISO, MOSI, and GND for programming the chip. Once it’s programmed, it doesn’t need to be programmed again. Although I wrote the code for an ATMega48, it works fine on a pin-compatible ATMega8 which is pictured here. The connector at the top is that FTDI USB cable, and it supplies power and USB serial connectivity to the board.

If you look closely, you can see that modified code has been loaded on this board with a Linux laptop. This thing is an exciting little board, because it has so many possibilities. It could read voltages of a single channel in extremely high speed and send that data continuously, or it could read from many channels and send it at any rate, or even cooler would be to add some bidirectional serial communication capabilities to allow the computer to tell the microcontroller which channels to read and how often to report the values back. There is a lot of potential for this little design, and I’m glad I have it working.

Unfortunately I lost the schematics to this device because I formatted the computer that had the Eagle files on it. It should be simple and intuitive enough to be able to design again. The code for the microcontroller and code for the real-time visualization software will be posted below shortly. Below are some videos of this board in use in one form or another:

Here is the code that is loaded onto the microcontroller:

#define F_CPU 8000000UL
#include <avr/io.h>
#include <util/delay.h>

void readADC(char adcn){
		//ADMUX = 0b0100000+adcn; // AVCC ref on ADCn
		ADMUX = 0b1100000+adcn; // AVCC ref on ADCn
		ADCSRA |= (1<<ADSC); // reset value
        while (ADCSRA & (1<<ADSC)) {}; // wait for measurement
}

int main (void){        
    DDRD=255;
	init_usart();
    ADCSRA = 0b10000111; //ADC Enable, Manual Trigger, Prescaler
    ADCSRB = 0; 
    
    int adcs[8]={0,0,0,0,0,0,0,0};
    
    char i=0;
	for(;;){
		for (i=0;i<8;i++){readADC(i);adcs[i]=ADC>>6;}
		for (i=0;i<5;i++){sendNum(adcs[i]);send(44);}
		readADC(0);
		send(10);// LINE BREAK
		send(13); //return
		_delay_ms(3);_delay_ms(5);
	}
}

void sendNum(unsigned int num){
	char theIntAsString[7];
	int i;
	sprintf(theIntAsString, "%u", num);
	for (i=0; i < strlen(theIntAsString); i++){
		send(theIntAsString[i]);
	}
}


void send (unsigned char c){
	while((UCSR0A & (1<<UDRE0)) == 0) {}
	UDR0 = c;
}

void init_usart () {
	// ATMEGA48 SETTINGS
	int BAUD_PRESCALE = 12;
	UBRR0L = BAUD_PRESCALE; // Load lower 8-bits
	UBRR0H = (BAUD_PRESCALE >> 8); // Load upper 8-bits
	UCSR0A = 0;
	UCSR0B = (1<<RXEN0)|(1<<TXEN0); //rx and tx
	UCSR0C = (1<<UCSZ01) | (1<<UCSZ00); //We want 8 data bits
}

Here is the code that runs on the computer, allowing reading and real-time graphing of the serial data. It’s written in Python and has been tested in both Linux and Windows. It requires *NO* non-standard python libraries, making it very easy to distribute. Graphs are drawn (somewhat inefficiently) using lines in TK. Subsequent development went into improving the visualization, and drastic improvements have been made since this code was written, and updated code will be shared shortly. This is functional, so it’s worth sharing.

import Tkinter, random, time
import socket, sys, serial

class App:

	def white(self):
		self.lines=[]
		self.lastpos=0

		self.c.create_rectangle(0, 0, 800, 512, fill="black")
		for y in range(0,512,50):
			self.c.create_line(0, y, 800, y, fill="#333333",dash=(4, 4))
			self.c.create_text(5, y-10, fill="#999999", text=str(y*2), anchor="w")
		for x in range(100,800,100):
			self.c.create_line(x, 0, x, 512, fill="#333333",dash=(4, 4))
			self.c.create_text(x+3, 500-10, fill="#999999", text=str(x/100)+"s", anchor="w")

		self.lineRedraw=self.c.create_line(0, 800, 0, 0, fill="red")

		self.lines1text=self.c.create_text(800-3, 10, fill="#00FF00", text=str("TEST"), anchor="e")
		for x in range(800):
			self.lines.append(self.c.create_line(x, 0, x, 0, fill="#00FF00"))		

	def addPoint(self,val):
		self.data[self.xpos]=val
		self.line1avg+=val
		if self.xpos%10==0:
			self.c.itemconfig(self.lines1text,text=str(self.line1avg/10.0))
			self.line1avg=0
		if self.xpos>0:self.c.coords(self.lines[self.xpos],(self.xpos-1,self.lastpos,self.xpos,val))
		if self.xpos<800:self.c.coords(self.lineRedraw,(self.xpos+1,0,self.xpos+1,800))
		self.lastpos=val
		self.xpos+=1
		if self.xpos==800:
			self.xpos=0
			self.totalPoints+=800
			print "FPS:",self.totalPoints/(time.time()-self.timeStart)
		t.update()

	def __init__(self, t):
		self.xpos=0
		self.line1avg=0
		self.data=[0]*800
		self.c = Tkinter.Canvas(t, width=800, height=512)
		self.c.pack()
		self.totalPoints=0
		self.white()
		self.timeStart=time.time()

t = Tkinter.Tk()
a = App(t)

#ser = serial.Serial('COM1', 19200, timeout=1)
ser = serial.Serial('/dev/ttyUSB0', 38400, timeout=1)
sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
sock.setsockopt(socket.SOL_SOCKET, socket.SO_BROADCAST, 1)

while True:
	while True: #try to get a reading
		#print "LISTENING"
		raw=str(ser.readline())
		#print raw
		raw=raw.replace("\n","").replace("\r","")
		raw=raw.split(",")
		#print raw
		try:
			point=(int(raw[0])-200)*2
			break
		except:
			print "FAIL"
			pass
	point=point/2
	a.addPoint(point)

If you re-create this device of a portion of it, let me know! I’d love to share it on my website. Good luck!

Permanent link to this article: http://www.SWHarden.com/blog/2012-06-14-multichannel-usb-analog-sensor-with-atmega48/

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