Tour Pool 2015

Tour de France

My Tour Pool 2015 page is up! Check it out daily after each stage to see how terrible my team (Florky) is doing (as it does every year!).

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Flagstaff Mountain

Here are some photos from our hike today up Flagstaff Mountain. The kiddo really likes riding in the carrier!

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Small Hike

Today we went on a small hike to Fourmile Creek. Here are some photos and videos.


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Homemade Bike Rack Mount

Below are some photos of the homemade parts I made for the truck that my old bike rack can interface with. I used pieces of shelf rail that hold the Yakima feet, and attach the whole stack to the rails on the side of the bed. This arrangement allows me to dis/mount the rack in a minute or so, which is how things have worked on previous vehicles with the rack, and I'm happy that it can work the same here. It's not the prettiest thing, and I suppose I could paint them black so they blend in better. Anyway, they were about $250 cheaper than the "official" Yakima system, so a little unsophistication is acceptable.

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Loaner Chickens

We have some friends that, due to a change in their housing situation, are in need of someone to take on their chickens for a while. So, we now have 5 egg-laying chickens in our backyard! It should be an interesting challenge.

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Solar Powered Shed Lights

Here are some photos of the solar powered LED lights for our sheds. My father very generously put together the lights, battery, solar panel, and wiring, and shipped it out to us. Over the last couple days I installed them in the sheds.

Tilted aggressively for lower winter sun.

Wire from solar panel and between sheds

The battery fits in the gap between the wall and the roof

The lights are mounted above the doors

The switch is mounted just inside the door

The view at night -- the LEDs light up the sheds quite nicely! (The flash on the camera was off)

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Tour Pool 2014

Tour de France

My Tour Pool 2014 page is up! Check it out daily after each stage to see how terrible my team (Florky) is doing (as it does every year!).

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Slinging Rock

How do you get 20 tons of gravel from street level to a side yard without carrying it up by hand? With a Stone Slinger! In the first video, yes, the man is driving the truck with a remote control.

rocks

rocks

rocks

rocks

rocks

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15 Minutes By Bicycle From Our Front Door

View

Unfortunately, this is now about 40 minutes away, but the above view isn't too shabby.

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How I Got a 327x Speedup Of Some Python Code

I don't usually post code stuff on this blog, but I had some fun working on this and I wanted to share!

My colleague, Abhi, is processing data from an instrument collecting actual data from the real world (you should know that this is something I have never done!) and is having some problems with how long his analysis is taking. In particular, it is taking him longer than a day to analyze a day's worth of data, which is clearly an unacceptable rate of progress. One step in his analysis is to take the data from all ~30,000 frequency channels of the instrument, and calculate an average across a moving window 1,000 entries long. For example, if I had the list:

[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]

and I wanted to find the average over a window of length three, I'd get:

[1, 2, 3, 4, 5, 6, 7, 8]

Notice that I started by averaging [0, 1, 2]=>1, as this is the first way to come up with a window of three values. Similarly, the last entry is [7, 8, 9]=>8. Here is a simplified version of how Ahbi was doing it (all of the code snippets shown here are also available [here][1]):

def avg0(arr, l):
    # arr - the list of values
    # l - the length of the window to average over
    new = []
    for i in range(arr.size - l + 1):
        s = 0
        for j in range(i, l + i):
            s += j
        new.append(s / l)
    return new

This function is correct, but when we time this simple function (using an IPython Magic) we get:

# a is [0, 1, 2, ..., 29997, 29998, 29999]
a = np.arange(30000)
%timeit avg0(a, 1000)
1 loops, best of 3: 3.19 s per loop

Which isn't so horrible in the absolute sense -- 3 seconds isn't that long compared to how much time we all waste per day. However, I neglected to mention above that Abhi must do this averaging for nearly 9,000 chunks of data per collecting day. This means that this averaging step alone takes about 8 hours of processing time per day of collected data. This is clearly taking too long!

The next thing I tried is to take advantage of Numpy, which is a Python package that enables much faster numerical analysis than with vanilla Python. In this function I'm essentially doing the same thing as above, but using Numpy methods, including pre-allocating space, summing values using the accelerated Numpy .sum() function, and using the xrange() iterator, which is somewhat faster than plain range():

def avg1(arr, l):
    new = np.empty(arr.size - l + 1, dtype=arr.dtype)
    for i in xrange(arr.size - l + 1):
        new[i] = arr[i:l+i].sum() / l
    return new

This provides a healthy speed up of about a factor of eight:

%timeit avg1(a, 1000)
1 loops, best of 3: 405 ms per loop

But this still isn't fast enough; we've gone from 8 hours to just under an hour. We'd like to run this analysis in at most a few minutes. Below is an improved method that takes advantage of a queue, which is a programming construct that allows you to efficiently keep track of values you've seen before.

def avg2(arr, l):
    new = np.empty(arr.size - l + 1, dtype=arr.dtype)
    d = deque()
    s = 0
    i = 0
    for value in arr:
        d.append(value)
        s += value
        if len(d) == l:
            new[i] = s / l
            i += 1
        elif len(d) > l:
            s -= d.popleft()
            new[i] = s / l
            i += 1
    return new

And here we can see that we've cut our time down by another factor of 4:

%timeit avg2(a, 1000)
10 loops, best of 3: 114 ms per loop

This means that from 8 hours we're now down to roughly 13 minutes. Getting better, but still not great. What else can we try? I've been looking for an excuse to try out Numba, which is a tool that is supposed to help speed up numerical analysis in Python, so I decided to give it a shot. What makes Numba attractive is that with a single additional line, Numba can take a function and dramatically speed it up by seamlessly converting it into C and compiling it when needed. So let's try this on the first averaging function:

@jit(argtypes=[int32[:], int32], restype=int32[:])
def avg0_numba(arr, l):
    new = []
    for i in range(arr.size - l + 1):
        s = 0
        for j in range(i, l + i):
            s += j
        new.append(s / l)
    return np.array(new)

In the line beginning with @jit, all I have to do is describe the input and the output types, and it handles the rest. And here's the result:

%timeit avg0_numba(a, 1000)
10 loops, best of 3: 21.6 ms per loop

What is incredible here is that not only is this roughly 5 times faster than the queue method above, it's a ridiculous 147 times faster than the original method and only one line has been added. We've now reduced 8 hours to about 4 minutes. Not bad!

Let's try this on the second averaging method, which if you recall, was substantially better than the original method:

@jit(argtypes=[int32[:], int32], restype=int32[:])
def avg1_numba(arr, l):
    new = np.empty(arr.size - l + 1, dtype=arr.dtype)
    for i in xrange(arr.size - l + 1):
        new[i] = arr[i:l+i].sum() / l
    return new
%timeit avg1_numba(a, 1000)
1 loops, best of 3: 688 ms per loop

That's interesting! For some reason I don't understand, this is actually slower than the un-optimized version of avg1. Let's see if Numba can speed up the queue method:

@jit(argtypes=[int32[:], int32], restype=int32[:])
def avg2_numba(arr, l):
    new = np.empty(arr.size - l + 1, dtype=arr.dtype)
    d = deque()
    s = 0
    i = 0
    for value in arr:
        d.append(value)
        s += value
        if len(d) == l:
            new[i] = s / l
            i += 1
        elif len(d) > l:
            s -= d.popleft()
            new[i] = s / l
            i += 1
    return new
%timeit avg2_numba(a, 1000)
10 loops, best of 3: 77.5 ms per loop

This is somewhat better than before, but still not as fast as avg0_numba, which comes in at roughly 20ms. But what if I really try hard to optimize the queue method by using only Numpy arrays?

@jit(argtypes=[int32[:], int32], restype=int32[:])
def avg2_numba2(arr, l):
    new = np.empty(arr.size - l + 1, dtype=arr.dtype)
    d = np.empty(l + 1, dtype=arr.dtype)
    s = 0
    i = 0
    left = 0
    right = 0
    full = False
    for j in xrange(arr.size):
        d[right] = arr[j]
        s += arr[j]
        right = (right + 1) % (l+1)
        if not full and right == l:
            new[i] = s / l
            i += 1
            full = True
        elif full:
            s -= d[left]
            left = (left + 1) % (l+1)
            new[i] = s / l
            i += 1
    return new
%timeit avg2_numba2(a, 1000)
100 loops, best of 3: 9.77 ms per loop

A ha! That's even faster, and our 3.19s are now down to 9.77ms, an improvement of 327 times. The original 8 hours are now reduced to less than two minutes. I hope you've enjoyed this as much as I have!

Update:

After chatting with a couple of my colleagues, this appears to be the fastest way to do this kind of operation:

from scipy.signal import fftconvolve
import numpy as np
a = np.arange(30000)
b = np.ones(1000) / 1000.
%timeit fftconvolve(a, b, 'valid')
100 loops, best of 3: 6.25 ms per loop
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Bye Bye Google Reader

Here's what I see when I look at my Google Reader stats:

Since May 22, 2007 you have read a total of 291,781 items.

That count will go no higher.

Google has decided to retire Reader on July 1st. Reluctantly, I have decided that I will not be using Reader on my six year anniversary. As a test, for the last week I have been exclusively using tt-rss installed on this web server as a replacement. So far it has been working pretty well. It's not a perfect replacement for Reader, but Reader isn't a perfect replacement for what Reader used to be, either. And unlike Reader, since it's self-hosted, no one will be taking it away from me.

If you want an account on my server, and you are someone I know personally, don't heistate to ask!

Update: I no longer run tt-rss. As of late, I have been using Feedly.

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Yet Another Snowy Picture

You really need to click on the image and see the full-sized version!

Tour de France

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Christmas in Boulder, 2012

Melissa and Stephen at Dowdy Draw

We have a tradition (2010, 2011) of going for a hike on Christmas eve in Boulder. This year we decided to keep it easy and go for a stroll/hike (Melissa calls it a "strike") at Dowdy Draw open space south of Boulder.

Melissa and Stephen with the mountains

Yesterday evening it started snowing, and by this morning there was roughly eight inches of fluffy snow on the ground, giving us a true white Christmas!

A snowy panorama of Boulder

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Snowy NIST

Snowy NIST

It's been over five months since I last posted on this blog! It seems appropriate that I come back with the counterpoint to the last photo I posted, this time showing the snowy Flatirons fronted by NIST.

Who knows when I'll post next!

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Foggy Flatirons & New Commute

Cloudy Flatirons

Since we have moved to our new house at the other end of town, my ride to campus is a bit different. In some ways I don't like it as much as my old route because it is next to Broadway for most of the way. Broadway is a very busy street, it's noisy and unpleasant. My old route did go for a short while on a busy street, but most of the time it was on roads in quiet neighborhoods or on bike paths.

Note that I wrote "next to Broadway" above. In fact, my new route is almost entirely on grade-separated bike paths/sidewalks (it's legal here for adults to ride on sidewalks some places) or frontage roads next to Broadway, and I actually never ride on Broadway. The big bonus on my new route is that the views are far superior. Above is a photo of the view looking over NIST towards the fog-enshrouded Flatirons. They are not often covered in clouds like this, but it had rained heavily the day before and the air was still humid. Also note that the grass in the foreground is brown. Before our heavy rains we had two weeks of record-setting heat. It's been a feast or famine summer in Boulder.

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