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2020 January 11

First week of class W2020

Filed under: Circuits course — gasstationwithoutpumps @ 21:16
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I’ve just finished the first week of class for BME 51A (Applied Electronics for Bioengineers), and it has been a rather hectic week.

First, I had about 5 people sign up for the class at the last minute (from 56 to 61), which drove the BELS staff to having to do a lot of expensive last-minute purchasing of additional items for the parts kits.  It also meant that when we handed out the parts kits on Tuesday, several of them were incomplete and so more items had to be handed out during the Thursday lab period.  Since getting their kits, 2 students have dropped taking us down to 59, and one other has told me that they might drop (assuming that they can get a coherent plan together for an independent study to replace the course).  This enrollment is less than last year’s 82 students, but still a fairly large number, given that the BELS labs can only accommodate about 24 students.  I’m using two lab rooms for the first section and one for the second section, and have hired 3 group tutors (one for each lab room and time) to work along with me in the labs.

The first week’s labs consist of soldering headers onto the Teensy LC boards and installing software: Python with SciPy (using the Anaconda install), gnuplot, Arduino+Teensyduino, PteroDAQ.  For the first time in years, everyone got their soldering done within the allotted lab times!  I don’t know what was different this year that made it work as it was supposed to.  One thing that helped a little was that when students soldered the male headers on the wrong side of the boards (which happens every year, despite all the written, pictorial, and verbal warnings I can give), I had them cut apart the male headers to unsolder, then gave them new male headers to solder on.

Software installation is always a problem, because students are attempting to install on a variety of platforms, and something is always incompatible. Here are some problems that came up this year:

  • Gnuplot on old Mac OS X systems would not install with homebrew, as qt could not be installed—it insisted that you needed the full Xcode (not just the command-line subset), but Apple will not provide the full Xcode for such old, unsupported systems.  There may be already compiled versions of gnuplot for these old systems, but I have not gone looking for them. I’m not sure what to recommend to these students, other than updating to a system that Apple still supports.  I can’t recommend updating to Catalina, as they will lose all 32-bit apps, some of which will never be ported to newer versions of macos (for example, I lost access to Finale Notepad, which is no longer available on Macs—probably because Apple makes it so very difficult for third-party software developers to maintain their code).
  • Gnuplot on new Mac OS X systems installs and runs, but produces bad PDF files.  The workaround for this was posted at https://stackoverflow.com/questions/57698204/gnuplot-pdf-terminal-exhibits-font-issues-on-mac. The answer to that stackoverflow question had two lines to fix the problem:
    brew uninstall --ignore-dependencies pango
    brew install iltommi/brews/pango
    

    The problem is that the default homebrew “bottle” for gnuplot points to a broken version of pango, and you have to remove that version and install an older version.  This one I knew about, because it had bitten me when I was trying to finish the book in December.

  • The standard Arduino+Teensyduino installation fails on macos Catalina (10.15). I knew about this one also, as I had tested the PteroDAQ install after I had “upgraded” to Catalina (which broke nearly everything).  The workaround is a beta release of Teensyduino (currently https://forum.pjrc.com/threads/59030-Teensyduino-1-49-Beta-5), which is pointed to from the Teensyduino installation page, but many of the students with macos Catalina did not notice the pointer.  One nice feature of the Teensyduino beta release is that it includes the Arduino IDE, so that you don’t need to install Arduino first.
  • The PteroDAQ GUI seems to be crashing on macos Mojave (10.14)—logging the user out when they try to run “python daq” as usual.  I think that this may be a weird filesystem thing, as it seemed to make a difference whether PteroDAQ had been cloned from GitHub or downloaded as a zip file, and whether the files were on the hard drive or on a Google Drive.  The only thing that seemed to work consistently was to clone the files from GitHub onto the hard drive of the laptop, then run the app that is in pterodaq/extras/maclauncher/ .  Why the launcher app works, when invoking “python daq” directly from a terminal results in logging the user out, is a mystery to me.
  • On macos Catalina, PteroDAQ can’t find the board if it is connected to the laptop through a USB2 hub connected to a USB3 port (I ran into this problem on my laptop before classes started also).  Apple has once again scrambled their USB stack, and USB Serial no longer seems to be visible through a USB2 hub (though the USB device is visible, the serial interface does not seem to be).  This hasn’t caused a problem for any students yet, as direct connection to a USB3 port works ok, and connection from hubs on USBC ports seems to be ok (probably because they are USB3 and not USB2).
  • One student had trouble getting PteroDAQ to run on his Windows 8 machine, with the python program crashing on trying to access the list of ports.  No one else with Windows 8 was having trouble, and his machine was running extremely slowly (slower even than the ancient “Barbie” laptop that I used for testing Windows implementations of PteroDAQ), so I suspect he was having hardware or malware problems on his machine.

I think that nearly all the students got their software installed—at any rate, people left the lab early on Thursday and were not queuing up for installation help, as they had in previous years.  Only one student asked for installation help during Friday office hours (the one with the probably bad hardware or malware), and there were no requests on Piazza for help.  If I’m right that everyone got things installed, then we are well ahead of previous years.

On Thursday, before lab, one of the group tutors ran a tutorial session on \LaTeX, which about half the class attended.  That should help somewhat in the prelabs to be turned in on Monday.

I’ve changed grading logistics this year.  Rather than hiring just 2 graders, I hired 6, and rather than having them work whenever they have time, I have scheduled grading sessions where we get together and grade in the same room.  On Thursday, we took just over 2 hours (with 5 graders, counting me) to grade homework 1, and today 6 of us got homework 2 graded in about an hour.  I graded the first quiz by myself Wednesday night.  So far, we have managed to keep the turn-around time to about a day, which is much better than last year, when the 2 graders were overloaded.

Monday’s assignments will be stressing our grading system a bit, as we have a lot coming in, but I couldn’t schedule a grading session until Wednesday at noon.  I’m hoping that we can get both homework 3 and the first prelab graded before Thursday’s lab.  If necessary, we can just give a turned-in/not-turned-in grade for the first prelab, as they are turning in a more complete draft of the same prelab on Friday, but I’d much rather give them feedback so that they can correct mistakes before the Friday draft.

So far, the quiz and homework scores look pretty good, so I’m hopeful that this will be a high-performing class this year.  It would be really nice to give out more B+ (and even A-) grades and fewer C grades.  I’m keeping my fingers crossed (even though that makes typing the blog post hard).

2019 December 19

Macos 10.15 Catalina vs PteroDAQ

I had a serious scare today.

First, I found out that the software for my Analog Discovery 2 was crashing on the MacBook Air that I will be using for lectures and lab next quarter.  It behaved normally at first and then crashed for no discernible reason after a couple of minutes.  I figured that the problem was probably related to the macos “upgrades” I had done recently, so I checked the Digilent website, and they had just posted a new version of the software last week, addressing the changes that Apple had made to their USB stack (which broke almost all 3rd-party software and a fair amount of Apple’s own software).  I downloaded the new version of Waveforms from the Digilent site and everything worked again.

But any changes to the USB stack are likely to break the code that PteroDAQ uses for finding what devices are connected, so I checked PteroDAQ with my usual setup.  The GUI for PteroDAQ did not list the Teensy board as it used to do, and PteroDAQ couldn’t run!  I spent a long time with ioreg trying to figure out how to modify macgetports.py to find the device again.  The Teensy board was visible as an AppleUSBDevice and AppleUSBInterface, but not as an IOSerialBSDClient as it used to be.  I could not figure out how to open it as a serial port!

Now my usual setup involves going through a USB 2.0 hub (in the Cerebrus cable), so I dug around in my drawer of parts until I found a plain USB-micro data cable.  Hooking up the Teensy board directly with that cable did show an IOSerialBSDClient interface, and PteroDAQ worked fine.  So the problem is just that connections through the USB 2.0 hub are not made the same way they used to be—the serial connection no longer is visible the way it used to be.

I’ll enter an issue for this on the PteroDAQ GitHub, but I won’t try to fix it unless it turns out that modern USB C-USB 3 docks exhibit the same problem.

2019 December 3

Moved PteroDAQ from BitBucket to GitHub

Filed under: Circuits course — gasstationwithoutpumps @ 18:00
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As mentioned in BitBucket being killed by Atlassian, Atlassian is killing off all its Mercurial repositories in BitBucket, forcing people to change to git.  They provide no tools for moving the repository, so it is easier to move to GitHub than to stay with BitBucket.

I have successfully moved the repository (using Github’s “import repository” drop-down menu item under the “+” tab, and moved over the issues, using the python program from https://github.com/jeffwidman/bitbucket-issue-migration

Because the PteroDAQ wiki had only two files, I moved them to the new repository manually, renaming the Home.md to README.md and editing the files lightly to update any BitBucket links.

I’ve even updated the link on the sidebar of this blog to point to the new Github repository.  It would be useful if one of my readers could check that the new repository works and that the installation instructions are ok.  I had no trouble, but I’m the owner of the repository, which makes a difference.

The new repository is at https://github.com/karplus/PteroDAQ

2017 December 18

EKG without amplifier

Filed under: Circuits course,Data acquisition — gasstationwithoutpumps @ 18:24
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I have done a lot of EKG projects on this blog, mostly for the Applied Electronics course, where an EKG amplifier is Lab 12, but some just for fun. Today I decided to see whether one could do an EKG with just the Teensy LC board or just an Analog Discovery 2 USB oscilloscope.

The project was partly inspired by the Digilent post DIY ECG using a Analog Discovery 2 and LabVIEW, which I saw the title for and assumed that they were using just the USB oscilloscope.  It turns out that wasn’t what they meant—it is just a simple 6-op-amp EKG amplifier looked at with the USB oscilloscope.

The setup I tried was about as simple as you can get—I put on three electrodes wired up as Lead I (see earlier post for this configuration), connected the body electrode to ground, and the other two electrodes to the plus and minus leads of channel 1 of the Analog Discovery 2.

The signal I got was quite small (about 1mV) and buried in 60Hz noise:

The raw signal from the oscilloscope, sampling at 1200 Hz, shows some spiking from the pulse, but a lot of noise. The big R spike is only about 3 LSB, so quantization noise is a problem.

I ran the recording through a digital filter to bandpass filter it to 0.1Hz–100Hz and put in a notch from 58Hz to 62Hz. The 100Hz low-pass had the effect of averaging out the noise, producing a signal with much finer resolution than the raw ADC values:

After filtering, the EKG signal is fairly clear. I don’t recommend trying to use only a couple of the lower-order bits of an ADC, but it is surprising how much information can be recovered by the filter.

I also tried using a Teensy LC board running PteroDAQ, using the A10–A11 differential channel. I had to bias my body between 0V and 3.3V, so I used a pair of 120kΩ resistors (one to GND, one to 3.3V) to connect to the body electrode.

Once again the raw signal was not great:

The signal had less noise than the signal to the Analog Discovery 2, but the signal was smaller also, negating the value of the finer steps of the ADC on the Teensy LC.

Once again, digital filtering restored the signal:

The signal-to-noise ratio here looks a little worse than for the Analog Discovery 2, despite the raw signal looking cleaner.

I managed to get a cleaner signal for the Analog Discovery 2 by turning off the surge protector, so that there was no 60Hz current anywhere nearby. The results after filtering were no better (and possibly worse) than from the signal with the 60Hz interference, so I did not bother plotting them for this post.

My conclusion is that it is possible to get EKG signals without adding an amplifier, but you can only see the signal clearly if you do some filtering.  I’ll have to decide whether to recommend to students that they record signals directly from the EKG electrodes to get an idea what their amplifiers have to work with.

2017 June 25

Fidget spinners revisited

Filed under: Uncategorized — gasstationwithoutpumps @ 17:55
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In Fidget spinners, I wrote about measuring and modeling the acceleration of two fidget spinners, 5-spoke spinner that cost $6.90 made from plastic and brass and a 3-bladed spinner that cost $8.90 milled out of brass:

The 5-spoked wheel spinner weighs 32.88±0.03g, and the 3-spoke brass spinner weighs 61.14±0.02g.

The previous post looked only at the fidget spinners spinning vertically (that is, with a horizontal axis), but I had noticed in playing with the spinners that they seemed to have different drag in different orientations, so I redid the measurements with the spinners horizontal (that is, with a vertical axis). I had a somewhat harder time spinning the spinners fast with them horizontally mounted, as my makeshift support for the photointerrupter was a bit precarious.

The 5-spoke wheel seemed to run smoothly , but the fit suggests more dry friction and less fluid friction.

The 3-spoke spinner really does not like to spin horizontally.

To visualize the physics better, I tried making acceleration vs. velocity plots for the fitted models:

When holding the wheel horizontally, there seems to be mainly dry friction, almost independent of the speed of the spin.

The 3-spoke spinner has much worse drag at all speeds when held horizontally rather than vertically. The fluid drag seems to be about the same as before, but there is much larger dry friction component (possibly from brass-on-brass contact between the spinner and the axle caps).

As expected from fidgeting with the spinners, the 3-blade spinner has much more drag than the wheel, both horizontally and vertically. The change from mainly wet friction to mainly dry friction for the wheel was unexpected, though.

Update 2017 Jun 25 21:15:  My wife just pointed me to a Wired article: https://www.wired.com/2017/05/the-phyiscs-of-fidget-spinners/ which does a poorer job of the same thing I did. They sampled at a fixed rate, rather than recording time stamps on each rising edge, so they had much poorer time resolution, and they assumed constant acceleration (dry friction), which is only appropriate for low-quality bearings.

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