To celebrate, I would like to pose a few coding challenges on the use of this library, based on a fun geometric puzzle from cut-the-knot: Rhombus in Circles

Segments and are equal. Lines and intersect at Form four circumcircles: Prove that the circumcenters form a rhombus, with

Note that if this construction works, it must do so independently of translations, rotations and dilations. We may then assume that is the origin, that the segments have length one, and that for some parameters it is We let SymPy take care of the computation of circumcenters:

import sympy
from sympy import *

# Point definitions
M=Point(0,0)
A=Point(2,0)
B=Point(1,0)
a,theta=symbols('a,theta',real=True,positive=True)
C=Point((a+1)*cos(theta),(a+1)*sin(theta))
D=Point(a*cos(theta),a*sin(theta))

#Circumcenters
E=Triangle(A,C,M).circumcenter
F=Triangle(A,D,M).circumcenter
G=Triangle(B,D,M).circumcenter
H=Triangle(B,C,M).circumcenter

Finding that the alternate angles are equal in the quadrilateral is pretty straightforward:

In [11]: P=Polygon(E,F,G,H)

In [12]: P.angles[E]==P.angles[G]
Out[12]: True

In [13]: P.angles[F]==P.angles[H]
Out[13]: True

To prove it a rhombus, the two sides that coincide on each angle must be equal. This presents us with the first challenge: Note for example that if we naively ask SymPy whether the triangle is equilateral, we get a False statement:

In [14]: Triangle(E,F,G).is_equilateral()
Out[14]: False

In [15]: F.distance(E)
Out[15]: Abs((a/2 - cos(theta))/sin(theta) - (a - 2*cos(theta) + 1)/(2*sin(theta)))

In [16]: F.distance(G)
Out[16]: sqrt(((a/2 - cos(theta))/sin(theta) - (a - cos(theta))/(2*sin(theta)))**2 + 1/4)

Part of the reason is that we have not indicated anywhere that the parameter theta is to be strictly bounded above by (we did indicate that it must be strictly positive). The other reason is that SymPy does not handle identities well, unless the expressions to be evaluated are perfectly simplified. For example, if we trust the routines of simplification of trigonometric expressions alone, we will not be able to resolve this problem with this technique:

In [17]: trigsimp(F.distance(E)-F.distance(G),deep=True)==0
Out[17]: False

Finding that with SymPy is not that easy either. This is the second challenge.

How would the reader resolve this situation?

Instant SymPy Starter

Exercise 1 Let be a measurable space and suppose is a sequence of measurable functions in that converge almost everywhere to a function and such that the sequence of norms converges to . Prove that the sequence of integrals converges to the integral for every measurable set .

Proof: Note first that

Set then (which are non-negative functions) and apply Fatou’s Lemma to that sequence. We have then

which implies

It must then be . But this proves the statement, since

Exercise 2 Let be a finite measure space and let . Suppose that is a sequence of measurable functions in whose norms are uniformly bounded in and which converge almost everywhere to a function . Prove that the sequence converges to for all where is the conjugate exponent of .

Proof: The proof is very similar to the previous problem. We start by noticing that under the hypotheses of the problem,

If we prove that , we are done.

We will achieve this by using the convexity of , since in that case it is

hence,

Set then (which are non-negative functions) and apply Fatou’s Lemma as before.

Or more importantly: rear your children to become nice people, water those trees, and make sure that your books make a good impact.

I recently enjoyed the rare pleasure of having a child (my first!) and publishing a book almost at the same time. Since this post belongs in my professional blog, I will exclusively comment on the latter: Learning SciPy for Numerical and Scientific Computing, published by Packt in a series of technical books focusing on Open Source software.

Keep in mind that the book is for a very specialized audience: not only do you need a basic knowledge of Python, but also a somewhat advanced command of mathematics/physics, and an interest in engineering or scientific applications. This is an excerpt of the detailed description of the monograph, as it reads in the publisher’s page:

It is essential to incorporate workflow data and code from various sources in order to create fast and effective algorithms to solve complex problems in science and engineering. Data is coming at us faster, dirtier, and at an ever increasing rate. There is no need to employ difficult-to-maintain code, or expensive mathematical engines to solve your numerical computations anymore. SciPy guarantees fast, accurate, and easy-to-code solutions to your numerical and scientific computing applications.

Learning SciPy for Numerical and Scientific Computing unveils secrets to some of the most critical mathematical and scientific computing problems and will play an instrumental role in supporting your research. The book will teach you how to quickly and efficiently use different modules and routines from the SciPy library to cover the vast scope of numerical mathematics with its simplistic practical approach that is easy to follow.

The book starts with a brief description of the SciPy libraries, showing practical demonstrations for acquiring and installing them on your system. This is followed by the second chapter which is a fun and fast-paced primer to array creation, manipulation, and problem-solving based on these techniques.

The rest of the chapters describe the use of all different modules and routines from the SciPy libraries, through the scope of different branches of numerical mathematics. Each big field is represented: numerical analysis, linear algebra, statistics, signal processing, and computational geometry. And for each of these fields all possibilities are illustrated with clear syntax, and plenty of examples. The book then presents combinations of all these techniques to the solution of research problems in real-life scenarios for different sciences or engineering — from image compression, biological classification of species, control theory, design of wings, to structural analysis of oxides.

The book is also being sold online in Amazon, where it has been received with pretty good reviews. I have found other random reviews elsewhere, with similar welcoming comments:

• Artificial Intelligence in Motion by Marcel Caraciolo
• The Endeavour, by John D. Cook

Just for fun, and as a means to learn Julia, I will be attempting problems from the Project Euler coding exclusively in that promising computer language.

The first problem is very simple:

Multiples of 3 and 5
If we list all the natural numbers below 10 that are multiples of 3 or 5, we get 3, 5, 6 and 9. The sum of these multip les is 23.

Find the sum of all the multiples of 3 or 5 below 1000.

One easy-to-code way is by dealing with arrays:

julia> sum( filter( x->((x%3==0) | (x%5==0)), [1:999] ) )
233168

A much better way is to obtain it via summation formulas: Note that the sum of all multiples of three between one and 999 is given by

Similarly, the sum of all multiples of five between one and 995 is given by

Finally, we need to subtract the sum of the multiples of both three and five, since they have been counted twice. This sum is

The final sum is then,

• Problem 2: Even Fibonacci Numbers
• Problem 3: Largest Prime Factor

If a pyramid is 250 cubits high and the side of its base 360 cubits long, what is its seked?

---

Take half of 360; it makes 180. Multiply 250 so as to get 180; it makes of a cubit. A cubit is 7 palms. Multiply 7 by

The seked is palms [that is, ].

A’h-mose. The Rhind Papyrus. 33 AD

The image above presents one of the problems included in the Rhind Papyrus, written by the scribe Ahmes (A’h-mose) circa 33 AD. This is a description of all the hieroglyphs, as translated by August Eisenlohr:

The question for the reader, after going carefully over the English translation is: What does seked mean?

On January first, a pair of mice appeared in a house and bore six male mice and six female mice. At the end of January there are fourteen mice: seven male and seven female.

On the first of February, each of the seven pairs bore six male and six female mice, so that at the end of February there are ninety-eight mice in forty-nine pairs. From then on, each pair of mice bore six more pairs every month.

1. Find the number of mice at the end of December.
2. Assume that the length of each mouse is 4 sun. If all the mice line up, each biting the tail of the one in front, find the total length of mice

Jinkō-ki, 1715

Some thieves stole a long roll of silk cloth from a warehouse. In a bush far from the warehouse, they counted the length of the cloth. If each thief gets 6 hiki, then 6 hiki is left over, but if each thief takes 7 hiki then the last thief gets no cloth at all. Find the number of thieves and the length of the cloth.

Jinkō-ki, 1643

Let’s examine an easy puzzle on finding the different stone by using a balance:

You have four stones identical in size and appearance, but one of them is heavier than the rest. You have a set of scales (a balance): how many weights do you need to determine which stone is the heaviest?

This is a trivial problem, but I will use it to illustrate different ideas, definitions, and the connection to linear algebra needed to answer the harder puzzles below. Let us start by solving it in the most natural way:

1. Enumerate each stone from 1 to 4.
2. Set stones 1 and 2 on the left plate; set stones 3 and 4 on the right plate. Since one of the stones is heavier, it will be in the plate that tips the balance. Let us assume this is the left plate.
3. Discard stones 3 and 4. Put stone 1 on the left plate; and stone 2 on the right plate. The plate that tips the balance holds the heaviest stone.

This solution finds the stone in two weights. It is what we call adaptive measures: each measure is determined by the result of the previous. This is a good point to introduce an algebraic scheme to code the solution.

• The weights matrix: This is a matrix with four columns (one for each stone) and two rows (one for each weight). The entries of this matrix can only be or depending whether a given stone is placed on the left plate , on the right plate or in neither plate For example, for the solution given above, the corresponding matrix would be
  
• The stones matrix: This is a square matrix with four rows and columns (one for each stone). Each column represents a different combination of stones, in such a way that the n-th column assumes that the heaviest stone is in the n-th position. The entries on this matrix indicate the weight of each stone. For example, if we assume that the heaviest stone weights b units, and each other stone weights a units, then the corresponding stones matrix is
  

Multiplying these two matrices, and looking at the sign of the entries of the resulting matrix, offers great insight on the result of the measures:

Note the columns of this matrix code the behavior of the measures:

• The column indicates that the balance tipped to the left in both measures (and therefore, the heaviest stone is the first one)
• The column indicates that the heaviest stone is the second one.
• Note that the other two measures can’t find the heaviest stone, since this matrix was designed to find adaptively a stone supposed to be either the first or the second.

Is it possible to design a solution to this puzzle that is not adaptive? Note the solution with two measures given (in algebraic form) below:

Since each column is different, it is trivial to decide after the experiment is done, which stone will be the heaviest. For instance, if the balance tips first to the right (-) and then to the left (+), the heaviest stone can only be the third one.

Let us make it a big harder: Same situation, but now we don’t know whether the stone that is different is heavier or lighter.

The solution above is no good: Since we are not sure whether b is greater or smaller than a, we would obtain two sign matrices which are virtually mirror images of each other.

and

In this case, in the event of obtaining that the balance tips twice to the left: which would be the different stone? The first, which is heaviest, or the fourth, which is lightest? We cannot decide.

One possible solution to this situation involves taking one more measure. Look at the algebraic expression of the following example, to realize why:

or

In this case there is no room for confusion: if the balance tips three times to the same side, then the different stone is the first one (whether heavier or lighter). The other possibilities are also easily solvable: if the balance tips first to one side, then to the other, and then to the first side, then the different stone is the third one.

The reader will not be very surprised at this point to realize that three (non adaptive) measures are also enough to decide which stone is different (be it heavier or lighter) in a set of twelve similar stones. To design the solution, a good weight matrix with twelve columns and three rows need to be constructed. The trick here is to allow measures that balance both plates, which gives us more combinations with which to play. How would the reader design this matrix?

As the title suggests (Modeling Nanoscale Imaging in Electron Microscopy), this book presents some recent advances that have been made using mathematical methods to resolve problems in electron microscopy. With improvements in hardware-based aberration software significantly expanding the nanoscale imaging capabilities of scanning transmission electron microscopes (STEM), these mathematical models can replace some labor intensive procedures used to operate and maintain STEMs. This book, the first in its field since 1998, covers relevant concepts such as super-resolution techniques (that’s my contribution!), special de-noising methods, application of mathematical/statistical learning theory, and compressed sensing.

We even got a nice review in Physics Today by Les Allen, no less!

Imaging with electrons, in particular scanning transmission electron microscopy (STEM), is now in widespread use in the physical and biological sciences. And its importance will only grow as nanotechnology and nano-Biology continue to flourish. Many applications of electron microscopy are testing the limits of current imaging capabilities and highlight the need for further technological improvements. For example, high throughput in the combinatorial chemical synthesis of catalysts demands automated imaging. The handling of noisy data also calls for new approaches, particularly because low electron doses are used for sensitive samples such as biological and organic specimens.

Modeling Nanoscale Imaging in Electron Microscopy addresses all those issues and more. Edited by Thomas Vogt and Peter Binev at the University of South Carolina (USC) and Wolfgang Dahmen at RWTH Aachen University in Germany, the book came out of a series of workshops organized by the Interdisciplinary Mathematics Institute and the NanoCenter at USC. Those sessions took the unusual but innovative approach of bringing together electron microscopists, engineers, physicists, mathematicians, and even a philosopher to discuss new strategies for image analysis in electron microscopy.

In six chapters, the editors tackle the ambitious challenge of bridging the gap between high-level applied mathematics and experimental electron microscopy. They have met the challenge admirably. I believe that high-resolution electron microscopy is at a point where it will benefit considerably from an influx of new mathematical approaches, daunting as they may seem; in that regard Modeling Nanoscale Imaging in Electron Microscopy is a major step forward. Some sections present a level of mathematical sophistication seldom encountered in the experimentally focused electron-microscopy literature.
The first chapter, by philosopher of science Michael Dickson, looks at the big picture by raising the question of how we perceive nano-structures and suggesting that a Kantian approach would be fruitful. The book then moves into a review of the application of STEM to nanoscale systems, by Nigel Browning, a leading experimentalist in the field, and other well-known experts. Using case studies, the authors show how beam-sensitive samples can be studied with high spatial resolution, provided one controls the beam dose and establishes the experimental parameters that allow for the optimum dose.

The third chapter, written by image-processing experts Sarah Haigh and Angus Kirkland, addresses the reconstruction, from atomic-resolution images, of the wave at the exit surface of a specimen. The exit surface wave is a fundamental quantity containing not only amplitude (image) information but also phase information that is often intimately related to the atomic-level structure of the specimen. The next two chapters, by Binev and other experts, are based on work carried out using the experimental and computational resources available at USC. Examples in chapter four address the mathematical foundations of compressed sensing as applied to electron microscopy, and in particular high-angle annular dark-field STEM. That emerging approach uses randomness to extract the essential content from low-information signals. Chapter five eloquently discusses the efficacy of analyzing several low-dose images with specially adapted digital-image-processing techniques that allow one to keep the cumulative electron dose low and still achieve acceptable resolution.

The book concludes with a wide-ranging discussion by mathematicians Amit Singer and Yoel Shkolnisky on the reconstruction of a three-dimensional object via projected data taken at random and initially unknown object orientations. The discussion is an extension of the authors’ globally consistent angular reconstitution approach for recovering the structure of a macromolecule using cryo-electron microscopy. That work is also applicable to the new generation of x-ray free-electron lasers, which have similar prospective applications, and illustrates nicely the importance of applied mathematics in the physical sciences.

Modeling Nanoscale Imaging in Electron Microscopy will be an important resource for graduate students and researchers in the area of high-resolution electron microscopy.

(Les J. Allen, Physics Today, Vol. 65 (5), May, 2012)

Table of contents	Preface	Sample chapter