luispedro

#vim: set ts=4 sts=4 expandtab sw=4:
from sys import argv
import matplotlib as mpl
import matplotlib.pyplot as plt
from math import sqrt
mpl.rcdefaults()

_golden_mean = (sqrt(5)-1.)/2.

bronzetan = '#BD3600'

luispedro

import numpy as np
import mahotas
from scipy import ndimage

img = mahotas.imread('copy_cam1.jpg')
img = img.mean(2)
img = img.astype(float)
bead = img[433:443,495:512]
sy,sx = bead.shape

luispedro

\documentclass{article}
\usepackage{tikz}

\begin{document}
\begin{tikzpicture}

\node (theta) at (0,0) [circle, draw] {$\theta$};
\node (z) at (2,0) [circle, draw] {$z$};
\node (w) at (4,0) [circle, draw] {$w$};
\node (alpha) at (1,2) [circle, draw] {$\alpha$};

luispedro

# Load a sparse matrix.

import numpy as np
from scipy import sparse

def load_sparse(filename, dtype=np.float32):
    with file(filename) as input:
        ny,nx = input.readline().strip().split()
        nelems = int(input.readline().strip())

luispedro

import numpy as np
def insert_bit(array, index):
    inner = (index % 64)
    index //= 64
    array[index] |= (1 << inner)
    

def is_set(array, index):
    inner = (index % 64)
    index //= 64

luispedro

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luispedro

def is_ascii(s):
    '''
    ascii = is_ascii(s)

    Check whether a unicode string is ASCII
    '''
    try:
        s = s.encode('ascii')
        return True
    except UnicodeError:

luispedro

from os import path, mkdir, errno

def create_directories(dname):
    '''
    create_directories(dname)

    Recursively create directories.
    '''
    if dname.endswith('/'): dname = dname[:-1]
    head, tail = path.split(dname)

luispedro

Luis Pedro Coelho is a PhD candidate in computational biology at Carnegie
Mellon University. He is interested in computational biology that is both
theoretically well-grounded and yields insights into real systems. Luis has a
BS and MS in computer science from Instituto Superior Técnico. He is a
Fulbright Scholar and has won multiple awards for academic or research
excellence.

Outside academia, Luis has been involved in theatre (having produced the
student group at IST and starred in several productions), as well as received a
prize in a short story competition. He has taught computer usage in

luispedro

from __future__ import division, with_statement
import signal

__all__ = ['TimeOutError', 'timeout']

class TimeOutError(Exception):
    def __init__(self):
        Exception.__init__(self,'Timeout')

def _raise_TimeOut(sig, stack):