TDI Web Log

So, T-Mobile pushed the Android 1.5 update to me last Sunday (I think).  I installed it and subsequently had to record a video with the new Camcorder application.  It works well; but produces videos with the audio track in AMR format.  The standard ffmpeg distributed with Ubuntu doesn’t have AMR compiled in because the AMR codec isn’t liberated/free.  I followed Chez’ instructions with a few modifications to get a tweaked ffmpeg that will convert videos recorded with my G1 phone.

• Run the standard ffmpeg to get the configure options used to compile it.
• apt-get install libmp3lame-dev libgsm1-dev libshroedinger-dev libspeex-dev libtheora-dev libvorbis-dev libdc1395-22-dev.
• Download, unpack, configure [--prefix=/usr/local/amr], make && make install both libamr-nb and -wb.
• svn checkout svn://svn.mplayerhq.hu/ffmpeg/trunk ffmpeg-2009-06-02.
• configure [*], make && make install ffmpeg.
• export LD_LIBRARY_PATH=/usr/local/amr/lib:/usr/local/ffmpeg/lib:$LD_LIBRARY_PATH
• /usr/local/ffmpeg/bin/ffmpeg -i video.3gp -ar 44100 vide.mpg

[*] I ended up using the following configure command for ffmpeg:
./configure –enable-gpl –enable-postproc –enable-x11grab –prefix=/usr/local/ffmpeg –enable-avfilter –enable-avfilter-lavf –enable-libgsm –enable-libschroedinger –enable-libspeex –enable-libtheora –enable-libvorbis –enable-pthreads –disable-stripping –enable-libdc1394 –disable-armv5te –disable-armv6 –disable-armv6t2 –disable-armvfp –disable-neon –disable-altivec –disable-vis –enable-shared –disable-static –enable-libamr-nb –enable-libamr-wb –enable-nonfree –extra-cflags=-I/usr/local/amr/include –extra-ldflags=-L/usr/local/amr/lib

Its not very often that you get to go back to old designs and make improvements. Recently I got to rework a design from last year and build on the collective knowlege of 2 design teams and 3 design cycles.

Does practice make perfect? We shall see.

The first run.

Last year I got to build the electronics for a stationary bike racing system. The system had a large ballfield style clock with four hands that were run by these monster stepper motors The initial design was for two bikes done by Percor: a company that makes excercize equipment. Their design used these industrial (expensive and very bulky) cherry hall effect sensors which they loaned us for a race at Lance Armstrong’s bike shop in Austin (http://www.mellowjohnnys.com/). My job for that cycle was to replace Percor’s pic based board with a 4 bike setup.

I broke the stepper driver section into four individual boards. For the processor I built a custom mega128 based board and did the programming in wiring.

Second iteration.

When the Austin race was over Percor needed their parts back so I got to rebuild the sensors. I found some allegra hall effect sensors which were a small fraction of the cost of the cherry’s (like (75c<$25.00)X4). As an attempt to get a zero indicator on the clock I experimented with a triangle based design

While I never did get this particular part of the clock to work correctly the triange stuck as a shape that I liked working with.

I also wanted to replace the cat5 wire used in the Percor design with with less expensive phone cord. (I got a panicked phone call  from Texas and had to remotely direct someone how to get some very expensive ethernet cable on a weekend: it was not cool). To do this I put a non inverting buffer on the sensors and since buffers come in 6s I put an indicator led on the sensors output. In the practice of setting this up for the next race, the blinking lights were invaluable.

Third Time Charm.

A few weeks ago I was asked about another race setup in SanFrancisco. They were going to use a system called open sprints for the display but the open sprints people were out of their hardware for the sensors. So I got a 3 week timeline to put together a sensor and hardware interface that would be compatible with open sprints.

Open sprints (www.opensprints.org) is an open source ruby based software which takes information from an arduino and presents the race data in a way that can be projected instead of having a physical race clock. The only thing that needed to be built was the input side.

So I went back to what I liked and didn’t like about my earlier design and compared and contrasted the opensprints, the percor and my designs to come up with a new system which I could then have fabbed by our local pcb fab (sunstone.com). Looking at the opensprints design I revisited the hall effect sensors and found a set of sensors to experiment with and began to lay out my boards.

I had intended to use the dart design with a through hole led and a throuch hole (sip) sensor and then have some laser cut transparent plastic which could then be “lit” up by the led on the board. A second piece of opaque plastic would be cut to insulate the bottom of the board.

After talking to some of my ee freinds I decided to replace the on board drivers with a single schmidt trigger on the other end of the sensor cable (the percor design used these as well) When selecting the parts I found myself looking at a few options for the rj11 connectors. I ordered a few of each as well as both sip and the origional smt sensor from last year.

Who needs plastic?

When I got the parts I started looking at these rj11 connectors and rethinking things. The connectors were surface mount and shielded. The shielding wasn’t needed but they matched the un-soldermasked boards in texture in color they were about 7 cents more expensive apiece but they looked futuristic.

I went back to surface mount only. If I got rid of the sips and used the surface mount rj11 mounts then the bottom of the board would be shield/ground no insulation needed. The metal from the surface of the board and cable connector would reflect the light from the led and if any attention were payed to the layout of the traces it would look cool!

Even in the hand rolled prototype!

Who needs an Arduino?

At this point given Paul Stoffregon’s (pjrc.com) “teensyduino” software and his 90usb based boards there is no reason to buy any other arduino or arduino clone. ( at least in cases where you need usb to serial solution — in cases where usb-serial is not needed the dorkboard rules My first thought was to do a carrier board for on of Paul’s boards and adapt the opensprints code for the inverted inputs. The opensprints code needs to be adapted to invert the input signal and to adjust the registers for the different processor but using the teensyquino codebase that should be simple enough.
In this application however, the board was so simple that it made more sense to just adopt the eagle design for my at90usb162 board (the benito).

Tomorrow I get the boards from sunstone and I should have the hardware built out by late friday. The customer will be in portland saturday.

Does practice make perfect? We will let you know by next week.

OK.  Since I stupidly spent too much time on this problem, I feel like I have to write about it here in the hopes that I can decrease the stupidity in the world.

I’ve written a GUI for a Matlab simulation.  On Linux, we use the JMatLink bridge between Java and Matlab.  At some point, when doing a dist-upgrade on my Ubuntu laptop, the JMatLink bridge stopped working, yielding the uninformative error:

Can't start MATLAB engine.

Well, I proceeded to hack JMatLink, turn on debugging for it, futzing with my LD_LIBRARY_PATH, and my PATH, changing JDKs (since there is a problem with the Sun JDKs and the X11 library libxcb (see here and here for more info on that — I finally downgraded to the gutsy libx11-6 and libx11-dev), etc.

In any case, my fog finally lifted and I decided to try the engdemo.c file provided by Mathworks as the canonical demonstration of calling Matlab from C. And, sure enough, I get the same uninformative error: Can’t start MATLAB engine.” So, I Ask.com’ed (no I don’t usually use the Eye of Sauron for searching) for URLs with this text in them and found: this post by “Mohammed Hasan”. Sure enough, I did an:

$ sudo apt-get install csh

and all is now well. [sigh]

Yesterday I asked Greg Borenstein what he was using to do his really cool Arduino presentations to show the hardware alongside the code being used to program it. His answer suprised me. It was a simple Quartz Composition run using Composer. He used it to flip the views put out by his web cam so that they made sense from the users viewpoint. I have been seeing a lot of people using quartz composer to do testing and other cool graphic things.

An example I have been working with takes a camera that I had on a pole with a motor that moved it around like a periscope. The camera is sideways so the view has to be rotated. I did this by hand using Core Image this summer using filters and transforms but wanted to do it in Quartz Composer. The composition looks like this.

And the resulting image like this.

On the way down to UCSF last month I experimented with some code that embeds a quartz composition into an application.

You can download it from our svn repository ( https://ssl.tempusdictum.com/pubsvn/trunks/QuartzSnap/ add this url to your x-code scm repositories) and play with it. It builds into a standalone application.

Most all of the work is done by adding your composition to the xcode project and then placing a Quartz Composer View (QCView) from the objects library in your window using Interface builder. The only code I needed to make my application usable (to take pictures) was the action to save the view to a file.

——————————– CameraViewController.h —————————-

#import <Cocoa/Cocoa.h>
#import <Quartz/Quartz.h>

@interface CameraViewController : NSObject {

IBOutlet NSButton *SnapButton;
IBOutlet QCView *CameraView;
NSImage    *TheSnapShot;
NSData *theSnapData;

}
- (IBAction)DoSnapShot:(id)sender;
@end

——————————– CameraViewController.m —————————-

#import "CameraViewController.h"

@implementation CameraViewController

- (IBAction)DoSnapShot:(id)sender {
   theSnapData = [[CameraView snapshotImage] TIFFRepresentation];
   int runResult;
   NSSavePanel *sp = [NSSavePanel savePanel];
   [sp setCanSelectHiddenExtension:YES];
   [sp setRequiredFileType:@"tif"];
   runResult = [sp runModalForDirectory:nil file:nil];
   if (runResult == NSOKButton) {
     if (![theSnapData writeToFile:[sp filename] atomically:YES])
       NSLog(@”Well that didn’t work!”);
   }
}

@end

And that is pretty much it.

Compared to the several pages of code it took to get the same results using Core Image this was a snap.

So, I inherited TDI’s MacBook from Cosmo who acquired a new one. He was nice enough to set up my user account with no password. Well, of course, that was untenable. So, I immediately set my password. … Time passed because I was occupied with other things. And, of course, I forgot the password. (As usual, this episode allowed the Mac vs. PC argument to bubble to the surface again. I rejoice in such arguments because diversity is the key to agility and dissent is the primary marker for diversity.)

Most websites claim you need an OS X install CD to reset the password. But, the helpful “Dr. Michael” showed us the unix way to do it, with which I’m so much more comfortable. In case that post disappears, here is a modified version of what he said that worked for me:

1. boot into single user mode (holding command s)
2. execute the two recommended commands
   
/sbin/fsck -fy <return>

   and
   
/sbin/mount -wu / <return>

3. type
   
passwd <username>

4. type the new password <return>
5. confirm the new password <return>
6. restart with
   
reboot <return>


I have a few devices that I need to interface to either the benito or another avr board that run at 3.3v. one is an ethernet interface, one is a bluetooth modem and then there are the x-bees.

One Way: Simple Voltage Divider.

When looking for interface examples for the xbee I found a site that started out with a circuit from maxstream and then once everything was working tried a resistor based voltage divider. This is how I got my first set of x-bees running via the ftdi chips.

One thing that this circuit didn’t do for me was to provide a decent pull-down for the reset. The 2 transistors on the right of this circuit are an attempt to do just that.

Another Way: Run everything at 3.3v

If you look at the datasheet for the atmega168 you will find the following diagram.

Looking at this you can see that 16mhz may or may not be in the operating range at 3.3v. But if you drop the crystal down to 8mhz you are good for sure. You may have to change a few things but it is doable.

The Ever Illusive Third: Buffers.

The idea of adding another layer at each interface between boards can have you asking for some Tzatziki and falafel to go with the PITA. There are buffers which are designed specifically for this. Many of the odd, many of them expensive. But there are also many families of buffer which are “tolerant” of a range of voltages outside of their supply. One of the buffers I checked out was the 74abt126 which is a tri state buffer. (I was looking at that because with the tristate buffers you can actually do a two way buffer by selecting the direction). I am not entirely certain that the 5v receive side is kosher with these.

The other buffers I am looking at with 5v tolerant i/o are the 74lvc125 and 74lvc126. These are 3.6v native parts with 5v “tolerant” io.

Since I ordered the wrong series of parts last group order I will have to wait a week to check this out.

See Also.

• Arduino Xbee Interface Circuit (AXIC)

We recently settled on Ubuntu as a common operating system for the machines on which we run biological models. That meant I have to reinstall Swarm and we encountered the same error Jim cites here.  Our failure is because the configure script doesn’t test for the amd64 platform.  I added the following lines to the configure (after line 19,539):

elif test -d ${jdkdir}/jre/lib/amd64/native_threads; then
threads=native
JAVACMD="\${jdkdir}/jre/bin/java"


That seems to have fixed our problem, perhaps it will help others who encounter the same error.

Finished assembling my CAVS from Critter and Guitari.

Here it is in action:

It’s more difficult than I expected to find a stable, interesting CA. But, although at first annoying, the audio helps find stable and interesting CAs.

As part of getting the new workspace space I moved the toxins related to casting and circuit board fabrication out of my apartment. The theory being that the space is semi industrial.

So as a test of the new space I took one of Alex Normans board designs and etched it.

Since the last time I worked with Alex on his designs he has picked up quite a bit and I only spent about 10 minutes getting his eagle files layed out and printed before going to the office. When I got there I realized that I had forgotten the green trf and bon ami but we were still able to get a reasonable etch and the new space has been broken in on the practice side.

Since TDI is such a wide ranging beast, we’ve created a more targeted website for the agent-based modeling work TDI does.  Check it out.

I’m almost ready to work here in our new “office”!

While I am wrangling with the appropriate board design, I needed to get started working with the underlying software so I ran up one of the six samples I was able to get from Cascade on a tqfp adapter from measure explorer.

The AtMega32U4 http://www.atmel.com/dyn/products/product_card.asp?part_id=4317 is the midrange model in the atmel usb chipset. It follows a new standard naming convention that atmel is adapting U for Usb 4 is for the 40 pins 32k, there is another 32K part the U6 which has the same pinouts as the 90usb646/647/1286/1287. The U4 does not have a legacy pinout however the q1000 price for this board is around $2 which makes it a very powerful chip for the money.

Dfu-Programmer.

There is a recent release of dfu-programmer (0.4.6) but it seems that they havent read the atmel doc on the signatures for the dfu recently. http://www.atmel.com/dyn/resources/prod_documents/doc7618.pdf recently.

I need to check the memory and eeprom sizes against the datasheets for the parts. However the table in arguments.c should have the following entries; added new parts, corrected 64x and 82 signatures. (I will resubmit this patch).

/* ----- target specific structures ----------------------------------------- */
/*  { "name",         value,            ,device_type, chipID,VID   , MemSize,FPSize,abt,ifclass,eepgsz,eepmemsz} */
static struct target_mapping_structure target_map[] = {
    { “at89c51snd1c”, tar_at89c51snd1c, device_8051, 0×2FFF, 0×03eb, 0×10000, 128, false, true,  0,   0      },
    { “at89c5130″,    tar_at89c5130,    device_8051, 0×2FFD, 0×03eb, 0×04000, 128, false, true,  128, 0×03FF },
    { “at89c5131″,    tar_at89c5131,    device_8051, 0×2FFD, 0×03eb, 0×08000, 128, false, true,  128, 0×03FF },
    { “at89c5132″,    tar_at89c5132,    device_8051, 0×2FFF, 0×03eb, 0×10000, 128, false, true,  0,   0      },
    { “at90usb1287″,  tar_at90usb1287,  device_AVR,  0×2FFB, 0×03eb, 0×1F000, 128, true,  false, 128, 0×0FFF },
    { “at90usb1286″,  tar_at90usb1286,  device_AVR,  0×2FFB, 0×03eb, 0×1F000, 128, true,  false, 128, 0×0FFF },
    { “at90usb647″,   tar_at90usb647,   device_AVR,  0×2FF9, 0×03eb, 0×0F000, 128, true,  false, 128, 0×07FF },
    { “at90usb646″,   tar_at90usb646,   device_AVR,  0×2FF9, 0×03eb, 0×0F000, 128, true,  false, 128, 0×07FF },
    { “atmega32U6″,   tar_atMega32u6,   device_AVR,  0×2FFB, 0×03eb, 0×07000, 128, true,  false, 128, 0×03FF },
    { “atmega32U4″,   tar_atMega32u4,   device_AVR,  0×2FF4, 0×03eb, 0×07000, 128, true,  false, 128, 0×03FF },
    { “atmega16U4″,   tar_atMega16u4,   device_AVR,  0×2FF3, 0×03eb, 0×03000, 128, true,  false, 128, 0×01FF },
    { “at90usb162″,   tar_at90usb162,   device_AVR,  0×2FFA, 0×03eb, 0×03000, 128, true,  false, 128, 0×01FF },
    { “at90usb82″,    tar_at90usb82,    device_AVR,  0×2FF7, 0×03eb, 0×01000, 128, true,  false, 128, 0×01FF },
    { NULL }
};

Then we test.

static
dfu-programmer atMega32U4 get bootloader-version --debug 20
     target: atMega32U4
    chip_id: 0x2ff4
  vendor_id: 0x03eb
    command: get
      quiet: false
      debug: 20
device_type: AVR
------ command specific below ------
       name: 0

Bootloader Version: 0x00 (0)

(after reading the datasheets for the 3 classes of avr usb chips and looking at the way that the avr-gcc library calls the cpu names there are some changes to the above that I will post later.)

Next up some code.

Tried running up the midiGate software that I wrote last week and found my first bug for the chip in avr-libc

UBRR1 is redefined in iom32u4.h

#define UBRR1 _SFR_MEM16(0xCC)

#define UBRR1L _SFR_MEM8(0xCC)
#define UBRR0 0
#define UBRR1 1
...

Which results in lvalue errors errors when trying to set the register to a given value. Setting the bit values as in some of the other registers seems to resolve this issue.

#define UBRR1 _SFR_MEM16(0xCC)

#define UBRR1L _SFR_MEM8(0xCC)
#define UBRR_0 0
#define UBRR_1 1
#define UBRR_2 2
#define UBRR_3 3
#define UBRR_4 4
#define UBRR_5 5
#define UBRR_6 6
#define UBRR_7 7

#define UBRR1H _SFR_MEM8(0xCD)
#define UBRR_8 0
#define UBRR_9 1
#define UBRR_10 2
#define UBRR_11 3

This is a pretty braindead error so I am sure that its been resolved by now. I need to see if it is fixed in 1.6.3 or the current release candidate (since AvrMacPack is out of sync and has 1.6.2) And yes this is the case.

We have a device!!!

Fix(ing) it!

Both of these issues were easy enough to fix within the source of the utilities but to make it possible for everyone else to use the new chips some body needs to Fix it! So I went about looking up the chain to get these issues resolved over the long run.

Dfu Programmer.

dfu-programmer is a source forge project so I logged an error through the sourceforge project page. https://sourceforge.net/tracker2/?atid=767783&group_id=147246&func=browse A new release has been made (0.5.0) which resolves the issue above.

Avr-Libc

Since avr-libc is a savanaha project and so making bug requests is a little different. http://savannah.nongnu.org/bugs/?group=avr-libc Fortunately (sort of) I had already been around the buggier parts of the release in question (1.6.2) when I first ran up the at90usb647. When Eric Weddington released the June rev of WinAvr (with avr-libc 1.6.3) I thought I had seen the last of it as obdev released the coresponding AvrMacPack. The bug noted above was fixed in 1.6.3 and I was able to verify that using my windows vmware session. For some reason this was not the case and AvrMacPack went out with the buggy (for this new chip anyway) libc. I filed a bug report with obdev and followed up with Christian from obdev and Eric until the version descrepency was resolved. The new version of WinAvr just came out and I am waiting to verify that the AvrMacPack version matches WinAvr.

If you are running linux plan on building from source and patching as in the script kept current at avrfreaks (you will need to log in) . http://www.avrfreaks.net/index.php?name=PNphpBB2&file=viewtopic&t=42631&start=0&postdays=0&postorder=asc&highlight= This script has not been updated for the latest winavr but it should at least give you a version above 1.6.2.

http://www.gearthblog.com/blog/archives/2008/10/google_earth_for_the_iphone_release.html

Our paper Enzyme Induction paper has finally been published!  Woohoo!

As usual, we’ll be participating (to some extent) in the ADS symposium.

The theme of ADS’09 is based on the observation of the following premises.

1. The growth of new advanced distributed computing standards along with the rapid rise of e-commerce are providing a new context that acts as a critical driver for the development of next generation systems. These standards revolve around service-oriented technologies, pervasive computing, web-services, Grid, autonomic computing, ambient intelligence etc. The supporting role that intelligent agents play in the development of such systems is becoming pervasive, and simulation plays a critical role in the analysis and design of such systems.
2. The use of emergent agent technologies at the organization, interaction (e.g., coordination, negotiation, communication) and agent levels (i.e. reasoning, autonomy) are expected to advance the state of the art in various application domains. However, modeling and testing complex agent systems that are based on such technologies is difficult. Using agent-supported simulation techniques for testing complex agent systems is up and coming field.
3. To facilitate bridging the gap between research and application, there is a need for tools, agent programming languages, and methodologies to analyze, design, and implement complex, non-trivial agent-based simulations. Existing agent-based simulation tools are still not mature enough to enable developing agents with varying degrees cognitive and reasoning capabilities.

Ethan and his dad came to the first dorkboard based induction. This is one of his recent projects.

http://etharooni.wordpress.com/2008/09/21/nunchucklogger/

Very cool stuff.

Brian Reilly at Wulfden picked up the dorkboard in his freeduino line of products.

http://wulfden.org/TheShoppe/freeduino/dorkboard.shtml

Yeah!

My partners got so excited about the ease with which one can create data-driven programs using QuartzComposer for the Mac that I just had to demonstrate to them that Apple doesn’t have any kind of lock on this domain. In fact, it brought to my mind a very old Mac OS 9 (or earlier I guess) visual programming language called Prograph, which has now become Marten and a handy little signal processing tool called Cantata, which has now become VisiQuest (look at the tutorials near the bottom of the page). And, of course, that’s not to mention the many other packages out there like PureData, LabView, etc.

Anyway, here’s my demonstration using Ptolemy II 7.0.1 over the top of FMJ (forget JMF - “Oh Sun Microsystems, why have you forsaken us?”):

At our company meeting, we were playing with a USB microscope Don borrowed from a friend of his. And one must admit that’s a much cooler thing to play with than a webcam. But, hey, my point can be made without the fancy hardware.

Things come in threes. I’m beginning to think that this “law of threes” might be a good gauge for when one should actually speak. Perhaps I’ll try it one day … just keep my mouth shut until there are 3 similar things about which to talk.

Anyway, I recently hosted a poster at the Engineering in Medicine and Biology Conference (EMBC) entitled: Using an In Silico Liver to Evaluate a Hepatic Enzyme Induction Mechanism. I won’t attempt to explain the contents, here (thank the gods, eh?); but the gist of it was that all models, including in silico (a.k.a. computational), in situ, in vitro, in vivo, indeed ALL ways of interacting with anything, involve what we’re calling a “phenomenal manifold” (a.k.a. an “aspect” as in Aspect-Oriented Programming). Basically, whenever a subject interacts with an object, the interaction is always mediated by some layer … a membrane. The subject cannot reach directly inside the object and manipulate or observe anything she might want to. Such interaction is always distorted, governed, or transduced through this layer. Granted, sometimes the layer can be very transparent so that it seems as if you’re touching the object directly. But in other cases, there are highly nonlinear or unpredictable effects when the subject manipulates the object or the data from observation can be very cryptic or misleading.

Why is this important? Well, in the context of using computational models to understand an extant system, the phenomenal manifold must be explicitly included in the experimental method. Otherwise, the results will not be repeatable and the effort can’t be considered “science”.

That’s the first of the three. The second is that one of us just got their hands on a high powered microscope and his family has been spending quite a bit of time staring at pond water animals through it. This sparked an argument between me and him about the telos of these animals’ motion. I suggested that it was primarily (say 70%) random, probably even Brownian (an aggregate of collisions with much smaller forces). He countered that their movements seem very purposeful, that they very clearly swim from place to place.

Now, I ran this by a few people, including biologists, and they all agree with him. The consensus seems to be that the motions of these animals do have telos and I am wrong. However, I maintain my skepticism primarily because this has the same texture as a mistake I’ve seen people make over and over again, never learning the lesson. We humans always ascribe telos. It is the fallacy of anthropocentrism. Besides, I can imagine many random, including Brownian-style, mechanisms that might generate seemingly purposeful behavior. So, as long as my imagined proto-hypothetical mechanisms are not falsified, my skepticism is appropriate and it’s just sloppy thinking to jump to the conclusion that the motions must be purposeful.

So that’s 2. And I was waiting for my partner to post some pictures or video about this locomotion to launch into the argument, here. But then the third thing came rattling down the pipe. I finally got caught up on my e-mail and, lo’ and behold, I find this post on Panda’s Thumb, wherein we find the telos-obsessed Intelligent Design people misquoting John von Neumann regarding the disturbing randomness at the heart of evolution. It’s useful to requote an excerpt of the quote used by Douglas to show that Berlinski misrepresented von Neuman.

Yet many efficient (?) and purposive (??) media, e.g., language, or the national economy, also look statistically controlled, when viewed from a suitably limited aspect.