### Archive

Posts Tagged ‘numpy’

## Robot stories

Every summer before school was over, I was assigned a list of books to read. Mostly nonfiction and historical fiction, but in fourth grade there that was that first science fiction book. I often remember how that book made me feel, and marvel at the impact that it had in my life. I had read some science fiction before—Well’s Time Traveller and War of the Worlds—but this was different. This was a book with witty and thought-provoking short stories by Isaac Asimov. Each of them delivered drama, comedy, mystery and a surprise ending in about ten pages. And they had robots. And those robots had personalities, in spite of their very simple programming: The Three Laws of Robotics.

1. A robot may not injure a human being or, through inaction, allow a human being to come to harm.
2. A robot must obey the orders given to it by human beings, except where such orders would conflict with the First Law.
3. A robot must protect its own existence as long as such protection does not conflict with the First or Second Law.

Back in the 1980s, robotics—understood as autonomous mechanical thinking—was no more than a dream. A wonderful dream that fueled many children’s imaginations and probably shaped the career choices of some. I know in my case it did.

Fast forward some thirty-odd years, when I met Astro: one of three research robots manufactured by the French company Aldebaran. This NAO robot found its way into the computer science classroom of Tom Simpson in Heathwood Hall Episcopal School, and quickly learned to navigate mazes, recognize some student’s faces and names, and even dance the Macarena! It did so with effortless coding: a basic command of the computer language python, and some idea of object oriented programming.

I could not let this opportunity pass. I created a small undergraduate team with Danielle Talley from USC (a brilliant sophomore in computer engineering, with a minor in music), and two math majors from Morris College: my Geometry expert Fabian Maple, and a McGyver-style problem solver, Wesley Alexander. Wesley and Fabian are supported by a Department of Energy-Environmental Management grant to Morris College, which funds their summer research experience at USC. Danielle is funded by the National Science Foundation through the Louis Stokes South Carolina-Alliance for Minority Participation (LS-SCAMP).

They spent the best of their first week on this project completing a basic programming course online. At the same time, the four of us reviewed some of the mathematical tools needed to teach Astro new tricks: basic algebra and trigonometry, basic geometry, and basic calculus and statistics. The emphasis—I need to point out in case you missed it—is in the word basic.

### Talk the talk

The psychologist seated herself and watched Herbie narrowly as he took a chair at the other side of the table and went through the three books systematically.

At the end of half an hour, he put them down, “Of course, I know why you brought these.”

The corner of Dr. Calvin’s lip twitched, “I was afraid you would. It’s difficult to work with you, Herbie. You’re always a step ahead of me.”

“It’s the same with these books, you know, as with the others. They just don’t interest me. There’s nothing to your textbooks. Your science is just a mass of collected data plastered together by makeshift theory — and all so incredibly simple, that it’s scarcely worth bothering about.”

“It’s your fiction that interests me. Your studies of the interplay of human motives and emotions” – his mighty hand gestured vaguely as he sought the proper words.

Liar!
— Isaac Asimov

Astro can understand what I say, and maintain conversations with me. He has four microphones for voice recognition and sound localization, and two speakers for text-to-speech synthesis. But he sometimes gets confused: I say “acute”, and he understands “abide,” for example. This might sound frustrating by all standards. But mathematicians can’t be judged by any reasonable standard. Far from seeing this as a shortcoming, my team used as motivation the mechanics behind his speech recognition functionality, and they wrote some code to turn him into an expert Mastermind player.

Wait, what? How are these two things possibly connected?

Since Astro’s hearing is far from perfect, when he hears a word which is not clear, he gathers a short list of possible candidates. He then chooses the most likely guess based upon different considerations—using clues from context, for example. Based on similar strategies, he can be taught to be a perfect player of 5-letter-word Mastermind: Pick any five-letter word in the English language. Any word, provided it has no repeated letters. Astro chooses one random word as his first guess, and requests a score like in Mastermind.

To illustrate this process, I will show you how the game went when I chose Fabian’s favorite word: “acute.”

Astro: Is it firth?
Me   : NO
Astro: How many letters of my guess are in your word, in the right position?
How many letters of my guess are in your word, in the wrong position?
Me   : 1, 0
Astro: Is it foams?
Me   : NO
Astro: How many letters of my guess are in your word, in the right position?
How many letters of my guess are in your word, in the wrong position?
Me   : 0, 1
Astro: Is it junta?
Me   : NO
Astro: How many letters of my guess are in your word, in the right position?
How many letters of my guess are in your word, in the wrong position?
Me   : 1, 2
Astro: Is it acute?
Me   : YES
Astro: Wonderful, I found it in 4 attempts!


I don’t want to get too technical here, but will mention some of the ideas. The main algorithm is based on techniques of numerical root finding and solving nonlinear equations — nothing complex: high-school level bracketing by bisection, or Newton’s method. To design better winning strategies, my team exploits the benefits of randomness. The analysis of this part is done with basic probability and statistics.

### Walk the walk

Donovan’s pencil pointed nervously. “The red cross is the selenium pool. You marked it yourself.”

“Which one is it?” interrupted Powell. “There were three that MacDougal located for us before he left.”

“I sent Speedy to the nearest, naturally; seventeen miles away. But what difference does that make?” There was tension in his voice. “There are penciled dots that mark Speedy’s position.”

And for the first time Powell’s artificial aplomb was shaken and his hands shot forward for the man.

“Are you serious? This is impossible.”

“There it is,” growled Donovan.

The little dots that marked the position formed a rough circle about the red cross of the selenium pool. And Powell’s fingers went to his brown mustache, the unfailing signal of anxiety.

Donovan added: “In the two hours I checked on him, he circled that damned pool four times. It seems likely to me that he’ll keep that up forever. Do you realize the position we’re in?”

Runaround
— Isaac Asimov

Astro moves around too. It does so thanks to a sophisticated system combining one accelerometer, one gyrometer and four ultrasonic sensors that provide him with stability and positioning within space. He also enjoys eight force-sensing resistors and two bumpers. And that is only for his legs! He can move his arms, bend his elbows, open and close his hands, or move his torso and neck (up to 25 degrees of freedom for the combination of all possible joints). Out of the box, and without much effort, he can be coded to walk around, although in a mechanical way: He moves forward a few feet, stops, rotates in place or steps to a side, etc. A very naïve way to go from A to B retrieving an object at C, could be easily coded in this fashion as the diagram shows:

Fabian and Wesley devised a different way to code Astro taking full advantage of his inertial measurement unit. This will allow him to move around smoothly, almost like a human would. The key to their success? Polynomial interpolation and plane geometry. For advanced solutions, they need to learn about splines, curvature, and optimization. Nothing they can’t handle.

### Sing me a song

He said he could manage three hours and Mortenson said that would be perfect when I gave him the news. We picked a night when she was going to be singing Bach or Handel or one of those old piano-bangers, and was going to have a long and impressive solo.

Mortenson went to the church that night and, of course, I went too. I felt responsible for what was going to happen and I thought I had better oversee the situation.

Mortenson said, gloomily, “I attended the rehearsals. She was just singing the same way she always did; you know, as though she had a tail and someone was stepping on it.”

One Night of Song
— Isaac Asimov

Astro has excellent eyesight and understanding of the world around him. He is equipped with two HD cameras, and a bunch of computer vision algorithms, including facial and shape recognition. Danielle’s dream is to have him read from a music sheet and sing or play the song in a toy piano. She is very close to completing this project: Astro is able now to identify partitures, and extract from them the location of the pentagrams. Danielle is currently working on identifying the notes and the clefs. This is one of her test images, and the result of one of her early experiments:

Most of the techniques Danielle is using are accessible to any student with a decent command of vector calculus, and enough scientific maturity. The extraction of pentagrams and the different notes on them, for example, is performed with the Hough transform. This is a fancy term for an algorithm that basically searches for straight lines and circles by solving an optimization problem in two or three variables.

The only thing left is an actual performance. Danielle will be leading Fabian and Wes, and with the assistance of Mr. Simpson’s awesome students Erica and Robert, Astro will hopefully learn to physically approach the piano, choose the right keys, and play them in the correct order and speed. Talent show, anyone?

## Math still not the answer

May 16, 2012 1 comment

I wrote a quick (but not very elegant) python script to retrieve locally enough data from www.metacritic.com for pattern recognition purposes. The main goal is to help me decide how much I will enjoy a movie, before watching it. I included the script at the end of the post, in case you want to try it yourself (and maybe improve it too!). It takes a while to complete, although it is quite entertaining to see its progress on screen. At the end, it provides with two lists of the same length: critics—a list of str containing the names of the critics; and scoredMovies—a list of dict containing, at index k, the evaluation of all the movies scored by the critic at index k in the previous list.

For example:

>>> critics[43]

‘James White’
>>> scoredMovies[43]

{‘hall-pass’: 60, ‘the-karate-kid’: 60, ‘the-losers’: 60,
‘the-avengers-2012’: 80, ‘the-other-guys’: 60, ‘shrek-forever-after’: 80,
‘the-lincoln-lawyer’: 80, ‘the-company-men’: 60, ‘jonah-hex’: 40,
‘arthur’: 60, ‘vampires-suck’: 20, ‘american-reunion’: 40,
‘footloose’: 60, ‘real-steel’: 60}

The number of scored films by critic varies: there are individuals that gave their opinion on a few dozen movies, and others that took the trouble to evaluate up to four thousand flicks! Note also that the names of the movies correspond with their web pages in www.metacritic.com. For example, to see what critics have to say about the “Karate Kid” and other relevant information online, point your browser to www.metacritic.com/movie/the-karate-kid. It also comes in very handy if there are several versions of a single title: Which “Karate Kid” does this score refer to, the one in the eighties, or Jackie Chan’s?

Feel free to download a copy of the resulting data [here] (note it is a large file: 1.6MB).

But the fact that we have that data stored locally allows us to gather that information with simple python commands, and perform many complex operations on it.

## Toying with basic fractals

I will skip all the mathematical theory behind Fractals (dimensions, measures, etc) to focus directly into the description and implementation of some of the most basic examples. In this post, I will cover the ideas behind three classical techniques:

• Iterated function systems
• Membership tests
• Lindenmayer systems

## Edge detection: The Scale Space Theory

Consider an image as a bounded function $f: \square_2 \to \mathbb{R}$ with no smoothness or structure assumptions a priori. Most relevant information of a given image is contained in the contours of the mapped objects: Think for example of a bright object against a dark background—the area where these two meet presents a curve where the intensity $f(\boldsymbol{x})$ varies strongly. This is what we refer to as an “edge.”

Initially, we may consider the process of detection of an edge by the simple computation of the gradient $\nabla f(\boldsymbol{x}) = \big( \tfrac{\partial f}{\partial x_1}, \tfrac{\partial f}{\partial x_2} \big):$ This gradient should have a large intensity $\lvert \nabla f(\boldsymbol{x}) \rvert$ and a direction $\tfrac{\nabla f(\boldsymbol{x})}{\lvert \nabla f(\boldsymbol{x}) \rvert}$ which indicates the perpendicular to the curve. It therefore looks sound to simply compute the gradient of $f$ and choose the points where these values are large. This conclusion is a bit unrealistic for two reasons:

1. The points where the gradient is larger than a given threshold are open sets, and thus don’t have the structure of curves.
2. Large gradient may arise in certain locations of the image due to tiny oscillations or noise, but completely unrelated to the objects being mapped. As a matter of fact, there is no reason to assume the existence or computability of any gradient at all in a given digital image.

## Voronoi mosaics

While looking for ideas to implement voronoi in sage, I stumbled upon a beautiful paper written by a group of japanese computer graphic professionals from the universities of Hokkaido and Tokyo: A Method for Creating Mosaic Images Using Voronoi Diagrams. The first step of their algorithm is simple yet brilliant: Start with any given image, and superimpose an hexagonal tiling of the plane. By a clever approximation scheme, modify the tiling to become a voronoi diagram that adaptively minimizes some approximation error. As a consequence, the resulting voronoi diagram is somehow adapted to the desired contours of the original image.

 (Fig. 1) (Fig. 2) (Fig. 3) (Fig. 4)

In a second step, they manually adjust the Voronoi image interactively by moving, adding, or deleting sites. They also take the liberty of adding visual effects by hand: emphasizing the outlines and color variations in each Voronoi region, so they look like actual pieces of stained glass (Fig. 4).

## Image Processing with numpy, scipy and matplotlibs in sage

In this post, I would like to show how to use  a few different features of numpy, scipy and matplotlibs to accomplish a few basic image processing tasks: some trivial image manipulation, segmentation, obtaining of structural information, etc.  An excellent way to show a good set of these techniques is by working through a complex project.  In this case, I have chosen the following:

Given a HAADF-STEM micrograph of a bronze-type Niobium Tungsten oxide $Nb_4W_{13}O_{47}$ (left), find a script that constructs a good approximation to its structural model (right).

 Courtesy of ETH Zurich

For pedagogical purposes, I took the following approach to solving this problem:

1. Segmentation of the atoms by thresholding and morphological operations.
2. Connected component labeling to extract each single atom for posterior examination.
3. Computation of the centers of mass of each label identified as an atom. This presents us with a lattice of points in the plane that shows a first insight in the structural model of the oxide.
4. Computation of Delaunay triangulation and Voronoi diagram of the previous lattice of points. The combination of information from these two graphs will lead us to a decent (approximation to the actual) structural model of our sample.

Let us proceed in this direction: