Shallow Thoughts

Akkana's Musings on Open Source Computing and Technology, Science, and Nature.

Wed, 20 Aug 2014

Mouse Release Movie

[Mouse peeking out of the trap] We caught another mouse! I shot a movie of its release.

Like the previous mouse we'd caught, it was nervous about coming out of the trap: it poked its nose out, but didn't want to come the rest of the way.

[Mouse about to fall out of the trap] Dave finally got impatient, picked up the trap and turned it opening down, so the mouse would slide out.

It turned out to be the world's scruffiest mouse, which immediately darted toward me. I had to step back and stand up to follow it on camera. (Yes, I know my camera technique needs work. Sorry.)

[scruffy mouse, just released from trap] [Mouse bounding away] Then it headed up the hill a ways before finally lapsing into the high-bounding behavior we've seen from other mice and rats we've released. I know it's hard to tell in the last picture -- the photo is so small -- but look at the distance between the mouse and its shadow on the ground.

Very entertaining! I don't understand why anyone uses killing traps -- even if you aren't bothered by killing things unnecessarily, the entertainment we get from watching the releases is worth any slight extra hassle of using the live traps.

Here's the movie: Mouse released from trap. [Mouse released from trap]

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[ 17:10 Aug 20, 2014    More nature | permalink to this entry | comments ]

Fri, 15 Aug 2014

Time-lapse photography: stitching movies together on Linux

[Time-lapse clouds movie on youtube] A few weeks ago I wrote about building a simple Arduino-driven camera intervalometer to take repeat photos with my DSLR. I'd been entertained by watching the clouds build and gather and dissipate again while I stepped through all the false positives in my crittercam, and I wanted to try capturing them intentionally so I could make cloud movies.

Of course, you don't have to build an Arduino device. A search for timer remote control or intervalometer will find lots of good options around $20-30. I bought one so I'll have a nice LCD interface rather than having to program an Arduino every time I want to make movies.

Setting the image size

Okay, so you've set up your camera on a tripod with the intervalometer hooked to it. (Depending on how long your movie is, you may also want an external power supply for your camera.)

Now think about what size images you want. If you're targeting YouTube, you probably want to use one of YouTube's preferred settings, bitrates and resolutions, perhaps 1280x720 or 1920x1080. But you may have some other reason to shoot at higher resolution: perhaps you want to use some of the still images as well as making video.

For my first test, I shot at the full resolution of the camera. So I had a directory full of big ten-megapixel photos with filenames ranging from img_6624.jpg to img_6715.jpg. I copied these into a new directory, so I didn't overwrite the originals. You can use ImageMagick's mogrify to scale them all:

mogrify -scale 1280x720 *.jpg

I had an additional issue, though: rain was threatening and I didn't want to leave my camera at risk of getting wet while I went dinner shopping, so I moved the camera back under the patio roof. But with my fisheye lens, that meant I had a lot of extra house showing and I wanted to crop that off. I used GIMP on one image to determine the x, y, width and height for the crop rectangle I wanted. You can even crop to a different aspect ratio from your target, and then fill the extra space with black:

mogrify img_6624.jpg -crop 2720x1450+135+315 -scale 1280 -gravity center -background black -extent 1280x720 *.jpg

If you decide to rescale your images to an unusual size, make sure both dimensions are even, otherwise avconv will complain that they're not divisible by two.

Finally: Making your movie

I found lots of pages explaining how to stitch together time-lapse movies using mencoder, and a few using ffmpeg. Unfortunately, in Debian, both are deprecated. Mplayer has been removed entirely. The ffmpeg-vs-avconv issue is apparently a big political war, and I have no position on the matter, except that Debian has come down strongly on the side of avconv and I get tired of getting nagged at every time I run a program. So I needed to figure out how to use avconv.

I found some pages on avconv, but most of them didn't actually work. Here's what worked for me:

avconv -f image2 -r 15 -start_number 6624 -i 'img_%04d.jpg' -vcodec libx264 time-lapse.mp4

Adjust the start_number and filename appropriately for the files you have.

Avconv produces an mp4 file suitable for uploading to youtube. So here is my little test movie: Time Lapse Clouds.

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[ 12:05 Aug 15, 2014    More photo | permalink to this entry | comments ]

Sat, 09 Aug 2014

Sphinx Moths

[White-lined sphinx moth on pale trumpets] We're having a huge bloom of a lovely flower called pale trumpets (Ipomopsis longiflora), and it turns out that sphinx moths just love them.

The white-lined sphinx moth (Hyles lineata) is a moth the size of a hummingbird, and it behaves like a hummingbird, too. It flies during the day, hovering from flower to flower to suck nectar, being far too heavy to land on flowers like butterflies do.

[Sphinx moth eye] I've seen them before, on hikes, but only gotten blurry shots with my pocket camera. But with the pale trumpets blooming, the sphinx moths come right at sunset and feed until near dark. That gives a good excuse to play with the DSLR, telephoto lens and flash ... and I still haven't gotten a really sharp photo, but I'm making progress.

Check out that huge eye! I guess you need good vision in order to make your living poking a long wiggly proboscis into long skinny flowers while laboriously hovering in midair.

Photos here: White-lined sphinx moths on pale trumpets.

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[ 21:23 Aug 09, 2014    More nature | permalink to this entry | comments ]

Tue, 05 Aug 2014

Privacy Policy

I got an envelope from my bank in the mail. The envelope was open and looked like the flap had never been sealed.

Inside was a copy of their privacy policy. Nothing else.

The policy didn't say whether their privacy policy included sealing the envelope when they send me things.

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[ 13:22 Aug 05, 2014    More humor | permalink to this entry | comments ]

Thu, 31 Jul 2014

Predicting planetary visibility with PyEphem

Part II: Predicting Conjunctions

After I'd written a basic script to calculate when planets will be visible, the next step was predicting conjunctions, times when two or more planets are close together in the sky.

Finding separation between two objects is easy in PyEphem: it's just one line once you've set up your objects, observer and date.

p1 = ephem.Mars()
p2 = ephem.Jupiter()
observer = ephem.Observer()  # and then set it to your city, etc.
observer.date = ephem.date('2014/8/1')
p1.compute(observer)
p2.compute(observer)

ephem.separation(p1, p2)

So all I have to do is loop over all the visible planets and see when the separation is less than some set minimum, like 4 degrees, right?

Well, not really. That tells me if there's a conjunction between a particular pair of planets, like Mars and Jupiter. But the really interesting events are when you have three or more objects close together in the sky. And events like that often span several days. If there's a conjunction of Mars, Venus, and the moon, I don't want to print something awful like

Friday:
  Conjunction between Mars and Venus, separation 2.7 degrees.
  Conjunction between the moon and Mars, separation 3.8 degrees.
Saturday:
  Conjunction between Mars and Venus, separation 2.2 degrees.
  Conjunction between Venus and the moon, separation 3.9 degrees.
  Conjunction between the moon and Mars, separation 3.2 degrees.
Sunday:
  Conjunction between Venus and the moon, separation 4.0 degrees.
  Conjunction between the moon and Mars, separation 2.5 degrees.

... and so on, for each day. I'd prefer something like:

Conjunction between Mars, Venus and the moon lasts from Friday through Sunday.
  Mars and Venus are closest on Saturday (2.2 degrees).
  The moon and Mars are closest on Sunday (2.5 degrees).

At first I tried just keeping a list of planets involved in the conjunction. So if I see Mars and Jupiter close together, I'd make a list [mars, jupiter], and then if I see Venus and Mars on the same date, I search through all the current conjunction lists and see if either Venus or Mars is already in a list, and if so, add the other one. But that got out of hand quickly. What if my conjunction list looks like [ [mars, venus], [jupiter, saturn] ] and then I see there's also a conjunction between Mars and Jupiter? Oops -- how do you merge those two lists together?

The solution to taking all these pairs and turning them into a list of groups that are all connected actually lies in graph theory: each conjunction pair, like [mars, venus], is an edge, and the trick is to find all the connected edges. But turning my list of conjunction pairs into a graph so I could use a pre-made graph theory algorithm looked like it was going to be more code -- and a lot harder to read and less maintainable -- than making a bunch of custom Python classes.

I eventually ended up with three classes: ConjunctionPair, for a single conjunction observed between two bodies on a single date; Conjunction, a collection of ConjunctionPairs covering as many bodies and dates as needed; and ConjunctionList, the list of all Conjunctions currently active. That let me write methods to handle merging multiple conjunction events together if they turned out to be connected, as well as a method to summarize the event in a nice, readable way.

So predicting conjunctions ended up being a lot more code than I expected -- but only because of the problem of presenting it neatly to the user. As always, user interface represents the hardest part of coding.

The working script is on github at conjunctions.py.

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[ 19:57 Jul 31, 2014    More science/astro | permalink to this entry | comments ]

Wed, 23 Jul 2014

Predicting planetary visibility with PyEphem

Part 1: Basic Planetary Visibility

All through the years I was writing the planet observing column for the San Jose Astronomical Association, I was annoyed at the lack of places to go to find out about upcoming events like conjunctions, when two or more planets are close together in the sky. It's easy to find out about conjunctions in the next month, but not so easy to find sites that will tell you several months in advance, like you need if you're writing for a print publication (even a club newsletter).

For some reason I never thought about trying to calculate it myself. I just assumed it would be hard, and wanted a source that could spoon-feed me the predictions.

The best source I know of is the RASC Observer's Handbook, which I faithfully bought every year and checked each month so I could enter that month's events by hand. Except for January and February, when I didn't have the next year's handbook yet by the time my column went to press and I was on my own. I have to confess, I was happy to get away from that aspect of the column when I moved.

In my new town, I've been helping the local nature center with their website. They had some great pages already, like a What's Blooming Now? page that keeps track of which flowers are blooming now and only shows the current ones. I've been helping them extend it by adding features like showing only flowers of a particular color, separating the data into CSV databases so it's easier to add new flowers or butterflies, and so forth. Eventually we hope to build similar databases of birds, reptiles and amphibians.

And recently someone suggested that their astronomy page could use some help. Indeed it could -- it hadn't been updated in about five years. So we got to work looking for a source of upcoming astronomy events we could use as a data source for the page, and we found sources for a few things, like moon phases and eclipses, but not much.

Someone asked about planetary conjunctions, and remembering how I'd always struggled to find that data, especially in months when I didn't have the RASC handbook yet, I got to wondering about calculating it myself. Obviously it's possible to calculate when a planet will be visible, or whether two planets are close to each other in the sky. And I've done some programming with PyEphem before, and found it fairly easy to use. How hard could it be?

Note: this article covers only the basic problem of predicting when a planet will be visible in the evening. A followup article will discuss the harder problem of conjunctions.

Calculating planet visibility with PyEphem

The first step was figuring out when planets were up. That was straightforward. Make a list of the easily visible planets (remember, this is for a nature center, so people using the page aren't expected to have telescopes):

import ephem

planets = [
    ephem.Moon(),
    ephem.Mercury(),
    ephem.Venus(),
    ephem.Mars(),
    ephem.Jupiter(),
    ephem.Saturn()
    ]

Then we need an observer with the right latitude, longitude and elevation. Elevation is apparently in meters, though they never bother to mention that in the PyEphem documentation:

observer = ephem.Observer()
observer.name = "Los Alamos"
observer.lon = '-106.2978'
observer.lat = '35.8911'
observer.elevation = 2286  # meters, though the docs don't actually say

Then we loop over the date range for which we want predictions. For a given date d, we're going to need to know the time of sunset, because we want to know which planets will still be up after nightfall.

observer.date = d
sunset = observer.previous_setting(sun)

Then we need to loop over planets and figure out which ones are visible. It seems like a reasonable first approach to declare that any planet that's visible after sunset and before midnight is worth mentioning.

Now, PyEphem can tell you directly the rising and setting times of a planet on a given day. But I found it simplified the code if I just checked the planet's altitude at sunset and again at midnight. If either one of them is "high enough", then the planet is visible that night. (Fortunately, here in the mid latitudes we don't have to worry that a planet will rise after sunset and then set again before midnight. If we were closer to the arctic or antarctic circles, that would be a concern in some seasons.)

min_alt = 10. * math.pi / 180.
for planet in planets:
    observer.date = sunset
    planet.compute(observer)
    if planet.alt > min_alt:
        print planet.name, "is already up at sunset"

Easy enough for sunset. But how do we set the date to midnight on that same night? That turns out to be a bit tricky with PyEphem's date class. Here's what I came up with:

    midnight = list(observer.date.tuple())
    midnight[3:6] = [7, 0, 0]
    observer.date = ephem.date(tuple(midnight))
    planet.compute(observer)
    if planet.alt > min_alt:
        print planet.name, "will rise before midnight"

What's that 7 there? That's Greenwich Mean Time when it's midnight in our time zone. It's hardwired because this is for a web site meant for locals. Obviously, for a more general program, you should get the time zone from the computer and add accordingly, and you should also be smarter about daylight savings time and such. The PyEphem documentation, fortunately, gives you tips on how to deal with time zones. (In practice, though, the rise and set times of planets on a given day doesn't change much with time zone.)

And now you have your predictions of which planets will be visible on a given date. The rest is just a matter of writing it out into your chosen database format.

In the next article, I'll cover planetary and lunar conjunctions -- which were superficially very simple, but turned out to have some tricks that made the programming harder than I expected.

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[ 21:32 Jul 23, 2014    More science/astro | permalink to this entry | comments ]

Wed, 16 Jul 2014

Time-lapse photography: a simple Arduino-driven camera intervalometer

[Arduino intervalometer] While testing my automated critter camera, I was getting lots of false positives caused by clouds gathering and growing and then evaporating away. False positives are annoying, but I discovered that it's fun watching the clouds grow and change in all those photos ... which got me thinking about time-lapse photography.

First, a disclaimer: it's easy and cheap to just buy an intervalometer. Search for timer remote control or intervalometer and you'll find plenty of options for around $20-30. In fact, I ordered one. But, hey, it's not here yet, and I'm impatient. And I've always wanted to try controlling a camera from an Arduino. This seemed like the perfect excuse.

Why an Arduino rather than a Raspberry Pi or BeagleBone? Just because it's simpler and cheaper, and this project doesn't need much compute power. But everything here should be applicable to any microcontroller.

My Canon Rebel Xsi has a fairly simple wired remote control plug: a standard 2.5mm stereo phone plug. I say "standard" as though you can just walk into Radio Shack and buy one, but in fact it turned out to be surprisingly difficult, even when I was in Silicon Valley, to find them. Fortunately, I had found some, several years ago, and had cables already wired up waiting for an experiment.

The outside connector ("sleeve") of the plug is ground. Connecting ground to the middle ("ring") conductor makes the camera focus, like pressing the shutter button halfway; connecting ground to the center ("tip") conductor makes it take a picture. I have a wired cable release that I use for astronomy and spent a few minutes with an ohmmeter verifying what did what, but if you don't happen to have a cable release and a multimeter there are plenty of Canon remote control pinout diagrams on the web.

Now we need a way for the controller to connect one pin of the remote to another on command. There are ways to simulate that with transistors -- my Arduino-controlled robotic shark project did that. However, the shark was about a $40 toy, while my DSLR cost quite a bit more than that. While I did find several people on the web saying they'd used transistors with a DSLR with no ill effects, I found a lot more who were nervous about trying it. I decided I was one of the nervous ones.

The alternative to transistors is to use something like a relay. In a relay, voltage applied across one pair of contacts -- the signal from the controller -- creates a magnetic field that closes a switch and joins another pair of contacts -- the wires going to the camera's remote.

But there's a problem with relays: that magnetic field, when it collapses, can send a pulse of current back up the wire to the controller, possibly damaging it.

There's another alternative, though. An opto-isolator works like a relay but without the magnetic pulse problem. Instead of a magnetic field, it uses an LED (internally, inside the chip where you can't see it) and a photo sensor. I bought some opto-isolators a while back and had been looking for an excuse to try one. Actually two: I needed one for the focus pin and one for the shutter pin.

How do you choose which opto-isolator to use out of the gazillion options available in a components catalog? I don't know, but when I bought a selection of them a few years ago, it included a 4N25, 4N26 and 4N27, which seem to be popular and well documented, as well as a few other models that are so unpopular I couldn't even find a datasheet for them. So I went with the 4N25.

Wiring an opto-isolator is easy. You do need a resistor across the inputs (presumably because it's an LED). 380Ω is apparently a good value for the 4N25, but it's not critical. I didn't have any 380Ω but I had a bunch of 330Ω so that's what I used. The inputs (the signals from the Arduino) go between pins 1 and 2, with a resistor; the outputs (the wires to the camera remote plug) go between pins 4 and 5, as shown in the diagram on this Arduino and Opto-isolators discussion, except that I didn't use any pull-up resistor on the output.

Then you just need a simple Arduino program to drive the inputs. Apparently the camera wants to see a focus half-press before it gets the input to trigger the shutter, so I put in a slight delay there, and another delay while I "hold the shutter button down" before releasing both of them.

Here's some Arduino code to shoot a photo every ten seconds:

int focusPin = 6;
int shutterPin = 7;

int focusDelay = 50;
int shutterOpen = 100;
int betweenPictures = 10000;

void setup()
{
    pinMode(focusPin, OUTPUT);
    pinMode(shutterPin, OUTPUT);
}

void snapPhoto()
{
    digitalWrite(focusPin, HIGH);
    delay(focusDelay);
    digitalWrite(shutterPin, HIGH);
    delay(shutterOpen);
    digitalWrite(shutterPin, LOW);
    digitalWrite(focusPin, LOW);
}

void loop()
{
    delay(betweenPictures);
    snapPhoto();
}

Naturally, since then we haven't had any dramatic clouds, and the lightning storms have all been late at night after I went to bed. (I don't want to leave my nice camera out unattended in a rainstorm.) But my intervalometer seemed to work fine in short tests. Eventually I'll make some actual time-lapse movies ... but that will be a separate article.

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[ 18:31 Jul 16, 2014    More hardware | permalink to this entry | comments ]

Sat, 12 Jul 2014

Trapped our first pack rat

[White throated woodrat in a trap] One great thing about living in the country: the wildlife. I love watching animals and trying to photograph them.

One down side of living in the country: the wildlife.

Mice in the house! Pack rats in the shed and the crawlspace! We found out pretty quickly that we needed to learn about traps.

We looked at traps at the local hardware store. Dave assumed we'd get simple snap-traps, but I wanted to try other options first. I'd prefer to avoid killing if I don't have to, especially killing in what sounds like a painful way.

They only had one live mousetrap. It was a flimsy plastic thing, and we were both skeptical that it would work. We made a deal: we'd try two of them for a week or two, and when (not if) they didn't work, then we'd get some snap-traps.

We baited the traps with peanut butter and left them in the areas where we'd seen mice. On the second morning, one of the traps had been sprung, and sure enough, there was a mouse inside! Or at least a bit of fur, bunched up at the far inside end of the trap.

We drove it out to open country across the highway, away from houses. I opened the trap, and ... nothing. I looked in -- yep, there was still a furball in there. Had we somehow killed it, even in this seemingly humane trap?

I pointed the open end down and shook the trap. Nothing came out. I shook harder, looked again, shook some more. And suddenly the mouse burst out of the plastic box and went HOP-HOP-HOPping across the grass away from us, bounding like a tiny kangaroo over tufts of grass, leaving us both giggling madly. The entertainment alone was worth the price of the traps.

Since then we've seen no evidence of mice inside, and neither of the traps has been sprung again. So our upstairs and downstairs mice must have been the same mouse.

But meanwhile, we still had a pack rat problem (actually, probably, white-throated woodrats, the creature that's called a pack rat locally). Finding no traps for sale at the hardware store, we went to Craigslist, where we found a retired wildlife biologist just down the road selling three live Havahart rat traps. (They also had some raccoon-sized traps, but the only raccoon we've seen has stayed out in the yard.)

We bought the traps, adjusted one a bit where its trigger mechanism was bent, baited them with peanut butter and set them in likely locations. About four days later, we had our first captive little brown furball. Much smaller than some of the woodrats we've seen; probably just a youngster.

[White throated woodrat bounding away] We drove quite a bit farther than we had for the mouse. Woodrats can apparently range over a fairly wide area, and we didn't want to let it go near houses. We hiked a little way out on a trail, put the trap down and opened both doors. The woodrat looked up, walked to one open end of the trap, decided that looked too scary; walked to the other open end, decided that looked too scary too; and retreated back to the middle of the trap.

We had to tilt and shake the trap a bit, but eventually the woodrat gathered up its courage, chose a side, darted out and HOP-HOP-HOPped away into the bunchgrass, just like the mouse had.

No reference I've found says anything about woodrats hopping, but the mouse did that too. I guess hopping is just what you do when you're a rodent suddenly set free.

I was only able to snap one picture before it disappeared. It's not in focus, but at least I managed to catch it with both hind legs off the ground.

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[ 12:05 Jul 12, 2014    More nature | permalink to this entry | comments ]

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