Sage Interactions

Post code that demonstrates the use of the interact command in Sage here. It should be easy to just scroll through and paste examples out of here into their own sage notebooks.If you have suggestions on how to improve interact, add them [:interactSuggestions: here] or email [email protected].

• [:interact/graph_theory:] - Graph Theory
• [:interact/calculus:] - Calculus
• [:interact/diffeq:] - Differential Equations

Linear Algebra

Numerical instability of the classical Gram-Schmidt algorithm

by Marshall Hampton (tested by William Stein, who thinks this is really nice!)

def GS_classic(a_list):
    '''
    Given a list of vectors or a matrix, returns the QR factorization using the classical (and numerically unstable) Gram-Schmidt algorithm.    
    '''
    if type(a_list) != list:
        cols = a_list.cols()
        a_list = [x for x in cols]
    indices = range(len(a_list))
    q = []
    r = [[0 for i in indices] for j in indices]
    v = [a_list[i].copy() for i in indices]
    for i in indices:
        for j in range(0,i):
            r[j][i] = q[j].inner_product(a_list[i])
            v[i] = v[i] - r[j][i]*q[j]
        r[i][i] = (v[i]*v[i])^(1/2)
        q.append(v[i]/r[i][i])
    q = matrix([q[i] for i in indices]).transpose()
    return q, matrix(r)
def GS_modern(a_list):
    '''
    Given a list of vectors or a matrix, returns the QR factorization using the 'modern' Gram-Schmidt algorithm.    
    '''
    if type(a_list) != list:
        cols = a_list.cols()
        a_list = [x for x in cols]
    indices = range(len(a_list))
    q = []
    r = [[0 for i in indices] for j in indices]
    v = [a_list[i].copy() for i in indices]
    for i in indices:
        r[i][i] = v[i].norm(2)
        q.append(v[i]/r[i][i])
        for j in range(i+1, len(indices)):
            r[i][j] = q[i].inner_product(v[j])
            v[j] = v[j] - r[i][j]*q[i]
    q = matrix([q[i] for i in indices]).transpose()
    return q, matrix(r)
html('<h2>Numerical instability of the classical Gram-Schmidt algorithm</h2>')
@interact
def gstest(precision = slider(range(3,53), default = 10), a1 = input_box([1,1/1000,1/1000]), a2 = input_box([1,1/1000,0]), a3 = input_box([1,0,1/1000])):
    myR = RealField(precision)
    displayR = RealField(5)
    html('precision in bits: ' + str(precision) + '<br>')
    A = matrix([a1,a2,a3])
    A = [vector(myR,x) for x in A]
    qn, rn = GS_classic(A)
    qb, rb = GS_modern(A)
    html('Classical Gram-Schmidt:')
    show(matrix(displayR,qn))
    html('Stable Gram-Schmidt:')
    show(matrix(displayR,qb))

attachment:GramSchmidt.png

Linear transformations

by Jason Grout

A square matrix defines a linear transformation which rotates and/or scales vectors. In the interact command below, the red vector represents the original vector (v) and the blue vector represents the image w under the linear transformation. You can change the angle and length of v by changing theta and r.

@interact
def linear_transformation(theta=slider(0, 2*pi, .1), r=slider(0.1, 2, .1, default=1)):
    A=matrix([[1,-1],[-1,1/2]])
    v=vector([r*cos(theta), r*sin(theta)])
    w = A*v
    circles = sum([circle((0,0), radius=i, rgbcolor=(0,0,0)) for i in [1..2]])
    print jsmath("v = %s,\; %s v=%s"%(v.n(4),latex(A),w.n(4)))
    show(v.plot(rgbcolor=(1,0,0))+w.plot(rgbcolor=(0,0,1))+circles,aspect_ratio=1)

attachment:Linear-Transformations.png

Singular value decomposition

by Marshall Hampton

import scipy.linalg as lin
var('t')
def rotell(sig,umat,t,offset=0):
    temp = matrix(umat)*matrix(2,1,[sig[0]*cos(t),sig[1]*sin(t)])
    return [offset+temp[0][0],temp[1][0]]
@interact
def svd_vis(a11=slider(-1,1,.05,1),a12=slider(-1,1,.05,1),a21=slider(-1,1,.05,0),a22=slider(-1,1,.05,1),ofs= selector(['Off','On'],label='offset image from domain')):
    rf_low = RealField(12)
    my_mat = matrix(rf_low,2,2,[a11,a12,a21,a22])
    u,s,vh = lin.svd(my_mat.numpy())
    if ofs == 'On': 
        offset = 3
        fsize = 6
        colors = [(1,0,0),(0,0,1),(1,0,0),(0,0,1)]
    else: 
        offset = 0
        fsize = 5
        colors = [(1,0,0),(0,0,1),(.7,.2,0),(0,.3,.7)]
    vvects = sum([arrow([0,0],matrix(vh).row(i),rgbcolor = colors[i]) for i in (0,1)])    
    uvects = Graphics()
    for i in (0,1):
        if s[i] != 0: uvects += arrow([offset,0],vector([offset,0])+matrix(s*u).column(i),rgbcolor = colors[i+2])
    html('<h3>Singular value decomposition: image of the unit circle and the singular vectors</h3>')
    print jsmath("A = %s  = %s %s %s"%(latex(my_mat), latex(matrix(rf_low,u.tolist())), latex(matrix(rf_low,2,2,[s[0],0,0,s[1]])), latex(matrix(rf_low,vh.tolist())))) 
    image_ell = parametric_plot(rotell(s,u,t, offset),0,2*pi)
    graph_stuff=circle((0,0),1)+image_ell+vvects+uvects
    graph_stuff.set_aspect_ratio(1)
    show(graph_stuff,frame = False,axes=False,figsize=[fsize,fsize])

attachment:svd1.png

Discrete Fourier Transform

by Marshall Hampton

import scipy.fftpack as Fourier
@interact
def discrete_fourier(f = input_box(default=sum([sin(k*x) for k in range(1,5,2)])), scale = slider(.1,20,.1,5)):
    var('x')
    pbegin = -float(pi)*scale
    pend = float(pi)*scale
    html("<h3>Function plot and its discrete Fourier transform</h3>")
    show(plot(f, pbegin, pend, plot_points = 512), figsize = [4,3])
    f_vals = [f(ind) for ind in srange(pbegin, pend,(pend-pbegin)/512.0)]
    my_fft = Fourier.fft(f_vals)
    show(list_plot([abs(x) for x in my_fft], plotjoined=True), figsize = [4,3])

attachment:dfft1.png

Algebra

Groebner fan of an ideal

by Marshall Hampton; (needs sage-2.11 or higher, with gfan-0.3 interface)

@interact
def gfan_browse(p1 = input_box('x^3+y^2',type = str, label='polynomial 1: '), p2 = input_box('y^3+z^2',type = str, label='polynomial 2: '), p3 = input_box('z^3+x^2',type = str, label='polynomial 3: ')):
    R.<x,y,z> = PolynomialRing(QQ,3)
    i1 = ideal(R(p1),R(p2),R(p3))
    gf1 = i1.groebner_fan()
    testr = gf1.render()    
    html('Groebner fan of the ideal generated by: ' + str(p1) + ', ' + str(p2) + ', ' + str(p3))
    show(testr, axes = False, figsize=[8,8*(3^(.5))/2])

attachment:gfan_interact.png

Number Theory

Factor Trees

by William Stein

import random
def ftree(rows, v, i, F):
    if len(v) > 0: # add a row to g at the ith level.
        rows.append(v)
    w = []
    for i in range(len(v)):
        k, _, _ = v[i]
        if k is None or is_prime(k):
            w.append((None,None,None))
        else:
            d = random.choice(divisors(k)[1:-1])
            w.append((d,k,i))
            e = k//d
            if e == 1:
                w.append((None,None))
            else:
                w.append((e,k,i))
    if len(w) > len(v):
        ftree(rows, w, i+1, F)
def draw_ftree(rows,font):
    g = Graphics()
    for i in range(len(rows)):
        cur = rows[i]
        for j in range(len(cur)):
            e, f, k = cur[j]
            if not e is None:
                if is_prime(e):
                     c = (1,0,0)
                else:
                     c = (0,0,.4)
                g += text(str(e), (j*2-len(cur),-i), fontsize=font, rgbcolor=c)
                if not k is None and not f is None:
                    g += line([(j*2-len(cur),-i), ((k*2)-len(rows[i-1]),-i+1)], 
                    alpha=0.5)
    return g

@interact
def factor_tree(n=100, font=(10, (8..20)), redraw=['Redraw']):
    n = Integer(n)
    rows = []
    v = [(n,None,0)]
    ftree(rows, v, 0, factor(n))
    show(draw_ftree(rows, font), axes=False)

attachment:factortree.png

Continued Fraction Plotter

by William Stein

@interact
def _(number=e, ymax=selector([None,5,20,..,400],nrows=2), clr=Color('purple'), prec=[500,1000,..,5000]):
    c = list(continued_fraction(RealField(prec)(number))); print c
    show(line([(i,z) for i, z in enumerate(c)],rgbcolor=clr),ymax=ymax,figsize=[10,2])

attachment:contfracplot.png

Illustrating the prime number thoerem

by William Stein

@interact
def _(N=(100,(2..2000))):
    html("<font color='red'>$\pi(x)$</font> and <font color='blue'>$x/(\log(x)-1)$</font> for $x < %s$"%N)
    show(plot(prime_pi, 0, N, rgbcolor='red') + plot(x/(log(x)-1), 5, N, rgbcolor='blue'))

attachment:primes.png

Computing Generalized Bernoulli Numbers

by William Stein (Sage-2.10.3)

@interact
def _(m=selector([1..15],nrows=2), n=(7,(3..10))):
    G = DirichletGroup(m)
    s = "<h3>First n=%s Bernoulli numbers attached to characters with modulus m=%s</h3>"%(n,m)
    s += '<table border=1>'
    s += '<tr bgcolor="#edcc9c"><td align=center>$\\chi$</td><td>Conductor</td>' + \
           ''.join('<td>$B_{%s,\chi}$</td>'%k for k in [1..n]) + '</tr>'
    for eps in G.list():
        v = ''.join(['<td align=center bgcolor="#efe5cd">$%s$</td>'%latex(eps.bernoulli(k)) for k in [1..n]])
        s += '<tr><td bgcolor="#edcc9c">%s</td><td bgcolor="#efe5cd" align=center>%s</td>%s</tr>\n'%(
             eps, eps.conductor(), v)
    s += '</table>'
    html(s)

attachment:bernoulli.png

Fundamental Domains of SL_2(ZZ)

by Robert Miller

L = [[-0.5, 2.0^(x/100.0) - 1 + sqrt(3.0)/2] for x in xrange(1000, -1, -1)]
R = [[0.5, 2.0^(x/100.0) - 1 + sqrt(3.0)/2] for x in xrange(1000)]
xes = [x/1000.0 for x in xrange(-500,501,1)]
M = [[x,abs(sqrt(x^2-1))] for x in xes]
fundamental_domain = L+M+R
fundamental_domain = [[x-1,y] for x,y in fundamental_domain]
@interact
def _(gen = selector(['t+1', 't-1', '-1/t'], nrows=1)):
    global fundamental_domain
    if gen == 't+1':
        fundamental_domain = [[x+1,y] for x,y in fundamental_domain]
    elif gen == 't-1':
        fundamental_domain = [[x-1,y] for x,y in fundamental_domain]
    elif gen == '-1/t':
        new_dom = []
        for x,y in fundamental_domain:
            sq_mod = x^2 + y^2
            new_dom.append([(-1)*x/sq_mod, y/sq_mod])
        fundamental_domain = new_dom
    P = polygon(fundamental_domain)
    P.ymax(1.2); P.ymin(-0.1)
    P.show()

attachment:fund_domain.png

Computing modular forms

by William Stein

j = 0
@interact
def _(N=[1..100], k=selector([2,4,..,12],nrows=1), prec=(3..40), 
      group=[(Gamma0, 'Gamma0'), (Gamma1, 'Gamma1')]):
    M = CuspForms(group(N),k)
    print j; global j; j += 1
    print M; print '\n'*3
    print "Computing basis...\n\n"
    if M.dimension() == 0:
         print "Space has dimension 0"
    else:
        prec = max(prec, M.dimension()+1)
        for f in M.basis():
             view(f.q_expansion(prec))
    print "\n\n\nDone computing basis."

attachment:modformbasis.png

Computing the cuspidal subgroup

by William Stein

html('<h1>Cuspidal Subgroups of Modular Jacobians J0(N)</h1>')
@interact
def _(N=selector([1..8*13], ncols=8, width=10, default=10)):
    A = J0(N)
    print A.cuspidal_subgroup()

attachment:cuspgroup.png

A Charpoly and Hecke Operator Graph

by William Stein

# Note -- in Sage-2.10.3; multiedges are missing in plots; loops are missing in 3d plots
@interact
def f(N = prime_range(11,400),
      p = selector(prime_range(2,12),nrows=1),
      three_d = ("Three Dimensional", False)):
    S = SupersingularModule(N)
    T = S.hecke_matrix(p)
    G = Graph(T, multiedges=True, loops=not three_d)
    html("<h1>Charpoly and Hecke Graph: Level %s, T_%s</h1>"%(N,p))
    show(T.charpoly().factor())
    if three_d:
        show(G.plot3d(), aspect_ratio=[1,1,1])
    else:
        show(G.plot(),figsize=7)

attachment:heckegraph.png

Demonstrating the Diffie-Hellman Key Exchange Protocol

by Timothy Clemans (refereed by William Stein)

@interact
def diffie_hellman(button=selector(["New example"],label='',buttons=True), 
    bits=("Number of bits of prime", (8,12,..512))):
    maxp = 2^bits
    p = random_prime(maxp)
    k = GF(p)
    if bits>100:
        g = k(2)
    else:
        g = k.multiplicative_generator()
    a = ZZ.random_element(10, maxp)
    b = ZZ.random_element(10, maxp)

    print """
<html>
<style>
.gamodp {
background:yellow
}
.gbmodp {
background:orange
}
.dhsame {
color:green;
font-weight:bold
}
</style>
<h2>%s-Bit Diffie-Hellman Key Exchange</h2>
<ol style="color:#000;font:12px Arial, Helvetica, sans-serif">
<li>Alice and Bob agree to use the prime number p=%s and base g=%s.</li>
<li>Alice chooses the secret integer a=%s, then sends Bob (<span class="gamodp">g<sup>a</sup> mod p</span>):<br/>%s<sup>%s</sup> mod %s = <span class="gamodp">%s</span>.</li>
<li>Bob chooses the secret integer b=%s, then sends Alice (<span class="gbmodp">g<sup>b</sup> mod p</span>):<br/>%s<sup>%s</sup> mod %s = <span class="gbmodp">%s</span>.</li>
<li>Alice computes (<span class="gbmodp">g<sup>b</sup> mod p</span>)<sup>a</sup> mod p:<br/>%s<sup>%s</sup> mod %s = <span class="dhsame">%s</span>.</li>
<li>Bob computes (<span class="gamodp">g<sup>a</sup> mod p</span>)<sup>b</sup> mod p:<br/>%s<sup>%s</sup> mod %s = <span class="dhsame">%s</span>.</li>
</ol></html>
    """ % (bits, p, g, a, g, a, p, (g^a), b, g, b, p, (g^b), (g^b), a, p, 
       (g^ b)^a, g^a, b, p, (g^a)^b)

attachment:dh.png

Plotting an elliptic curve over a finite field

E = EllipticCurve('37a')
@interact
def _(p=slider(prime_range(1000), default=389)):
    show(E)
    print "p = %s"%p
    show(E.change_ring(GF(p)).plot(),xmin=0,ymin=0)

attachment:ellffplot.png

Web applications

Stock Market data, fetched from Yahoo and Google

by William Stein

import urllib

class Day:
    def __init__(self, date, open, high, low, close, volume):
        self.date = date
        self.open=float(open); self.high=float(high); self.low=float(low); self.close=float(close)
        self.volume=int(volume)
    def __repr__(self):
        return '%10s %4.2f %4.2f %4.2f %4.2f %10d'%(self.date, self.open, self.high, 
                   self.low, self.close, self.volume)

class Stock:
    def __init__(self, symbol):
        self.symbol = symbol.upper()

    def __repr__(self):
        return "%s (%s)"%(self.symbol, self.yahoo()['price'])
    
    def yahoo(self):
        url = 'http://finance.yahoo.com/d/quotes.csv?s=%s&f=%s' % (self.symbol, 'l1c1va2xj1b4j4dyekjm3m4rr5p5p6s7')
        values = urllib.urlopen(url).read().strip().strip('"').split(',')
        data = {}
        data['price'] = values[0]
        data['change'] = values[1]
        data['volume'] = values[2]
        data['avg_daily_volume'] = values[3]
        data['stock_exchange'] = values[4]
        data['market_cap'] = values[5]
        data['book_value'] = values[6]
        data['ebitda'] = values[7]
        data['dividend_per_share'] = values[8]
        data['dividend_yield'] = values[9]
        data['earnings_per_share'] = values[10]
        data['52_week_high'] = values[11]
        data['52_week_low'] = values[12]
        data['50day_moving_avg'] = values[13]
        data['200day_moving_avg'] = values[14]
        data['price_earnings_ratio'] = values[15]
        data['price_earnings_growth_ratio'] = values[16]
        data['price_sales_ratio'] = values[17]
        data['price_book_ratio'] = values[18]
        data['short_ratio'] = values[19]
        return data

    def historical(self):
        try:
            return self.__historical
        except AttributeError:
            pass
        symbol = self.symbol
        def get_data(exchange):
             name = get_remote_file('http://finance.google.com/finance/historical?q=%s:%s&output=csv'%(exchange, symbol.upper()), 
                       verbose=False)
             return open(name).read()
        R = get_data('NASDAQ')
        if "Bad Request" in R:
             R = get_data("NYSE")
        R = R.splitlines()
        headings = R[0].split(',')
        self.__historical = []
        try:
            for x in reversed(R[1:]):
                date, opn, high, low, close, volume = x.split(',')
                self.__historical.append(Day(date, opn,high,low,close,volume))
        except ValueError:
             pass
        self.__historical = Sequence(self.__historical,cr=True,universe=lambda x:x)
        return self.__historical

    def plot_average(self, spline_samples=10):
        d = self.historical()
        if len(d) == 0:
            return text('no historical data at Google Finance about %s'%self.symbol, (0,3))
        avg = list(enumerate([(z.high+z.low)/2 for z in d]))
        P = line(avg) + points(avg, rgbcolor='black', pointsize=4) + \
                 text(self.symbol, (len(d)*1.05, d[-1].low), horizontal_alignment='right', rgbcolor='black')
        if spline_samples > 0:
            k = 250//spline_samples
            spl = spline([avg[i*k] for i in range(len(d)//k)] + [avg[-1]])
            P += plot(spl, (0,len(d)+30), color=(0.7,0.7,0.7))
        P.xmax(260)
        return P

    def plot_diff(self):
        d = self.historical()
        if len(d) == 0:
            return text('no historical data at Google Finance about %s'%self.symbol, (0,3))
        diff = [] 
        for i in range(1, len(d)):
             z1 = d[i]; z0 = d[i-1]
             diff.append((i, (z1.high+z1.low)/2 - (z0.high + z0.low)/2))
        P = line(diff,thickness=0.5) + points(diff, rgbcolor='black', pointsize=4) + \
                 text(self.symbol, (len(d)*1.05, 0), horizontal_alignment='right', rgbcolor='black')
        P.xmax(260)
        return P

symbols = ['bsc', 'vmw', 'sbux', 'aapl', 'amzn', 'goog', 'wfmi', 'msft', 'yhoo', 'ebay', 'java', 'rht', ]; symbols.sort()
stocks = dict([(s,Stock(s)) for s in symbols])

@interact
def data(symbol = symbols, other_symbol='', spline_samples=(8,[0..15])):
     if other_symbol != '':
         symbol = other_symbol
     S = Stock(symbol)
     html('<h1 align=center><font color="darkred">%s</font></h1>'%S)
     S.plot_average(spline_samples).save('avg.png', figsize=[10,2])
     S.plot_diff().save('diff.png', figsize=[10,2])

     Y = S.yahoo()
     k = Y.keys(); k.sort()
     html('Price during last 52 weeks:<br>Grey line is a spline through %s points (do not take seriously!):<br> <img src="cell://avg.png">'%spline_samples)
     html('Difference from previous day:<br> <img src="cell://diff.png">')
     html('<table align=center>' + '\n'.join('<tr><td>%s</td><td>%s</td></tr>'%(k[i], Y[k[i]]) for i in range(len(k))) + '</table>')

attachment:stocks.png

CO2 data plot, fetched from NOAA

by Marshall Hampton

While support for R is rapidly improving, scipy.stats has a lot of useful stuff too. This only scratches the surface.

import urllib2 as U
import scipy.stats as Stat
co2data = U.urlopen('ftp://ftp.cmdl.noaa.gov/ccg/co2/trends/co2_mm_mlo.txt').readlines()
datalines = []
for a_line in co2data:
    if a_line.find('Creation:') != -1:
        cdate = a_line
    if a_line[0] != '#':
        temp = a_line.replace('\n','').split(' ')
        temp = [float(q) for q in temp if q != '']
        datalines.append(temp)
trdf = RealField(16)
@interact
def mauna_loa_co2(start_date = slider(1958,2010,1,1958), end_date = slider(1958, 2010,1,2009)):
    htmls1 = '<h3>CO2 monthly averages at Mauna Loa (interpolated), from NOAA/ESRL data</h3>'
    htmls2 = '<h4>'+cdate+'</h4>'
    sel_data = [[q[2],q[4]] for q in datalines if start_date < q[2] < end_date]
    c_max = max([q[1] for q in sel_data])
    c_min = min([q[1] for q in sel_data])
    slope, intercept, r, ttprob, stderr = Stat.linregress(sel_data)
    html(htmls1+htmls2+'<h4>Linear regression slope: ' + str(trdf(slope)) + ' ppm/year; correlation coefficient: ' + str(trdf(r)) + '</h4>')
    var('x,y')
    show(list_plot(sel_data, plotjoined=True, rgbcolor=(1,0,0)) + plot(slope*x+intercept,start_date,end_date), xmin = start_date, ymin = c_min-2, axes = True, xmax = end_date, ymax = c_max+3, frame = False)

attachment:co2c.png

Pie Chart from the Google Chart API

by Harald Schilly

# Google Chart API: http://code.google.com/apis/chart
import urllib2 as inet
from pylab import imshow
@interact
def gChart(title="Google Chart API plots Pie Charts!", color1=Color('purple'), color2=Color('black'), color3=Color('yellow'), val1=slider(0,1,.05,.5), val2=slider(0,1,.05,.3), val3=slider(0,1,.05,0.1), label=("Maths Physics Chemistry")):
    url = "http://chart.apis.google.com/chart?cht=p3&chs=600x300"
    url += '&chtt=%s&chts=000000,25'%title.replace(" ","+")
    url += '&chco=%s'%(','.join([color1.html_color()[1:],color2.html_color()[1:],color3.html_color()[1:]]))
    url += '&chl=%s'%label.replace(" ","|")
    url += '&chd=t:%s'%(','.join(map(str,[val1,val2,val3])))
    print url
    html('<div style="border:3px dashed;text-align:center;padding:50px 0 50px 0"><img src="%s"></div>'%url)

attachment:interact_with_google_chart_api.png

Bioinformatics

Web app: protein browser

by Marshall Hampton (tested by William Stein)

import urllib2 as U
@interact
def protein_browser(GenBank_ID = input_box('165940577', type = str), file_type = selector([(1,'fasta'),(2,'GenPept')])):
    if file_type == 2:
        gen_str = 'http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&sendto=t&id='
    else:
        gen_str = 'http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&sendto=t&dopt=fasta&id='
    f = U.urlopen(gen_str + GenBank_ID)        
    g = f.read()
    f.close()
    html(g)

attachment:biobrowse.png

Coalescent simulator

by Marshall Hampton

def next_gen(x, selection=1.0):
    '''Creates the next generation from the previous; also returns parent-child indexing list'''
    next_x = []
    for ind in range(len(x)):
        if random() < (1 + selection)/len(x):
            rind = 0
        else:
            rind = int(round(random()*(len(x)-1)+1/2))
        next_x.append((x[rind],rind))
    next_x.sort()
    return [[x[0] for x in next_x],[x[1] for x in next_x]]
def coal_plot(some_data):
    '''Creates a graphics object from coalescent data'''
    gens = some_data[0]
    inds = some_data[1]
    gen_lines = line([[0,0]])
    pts = Graphics()
    ngens = len(gens)
    gen_size = len(gens[0])
    for x in range(gen_size):
        pts += point((x,ngens-1), hue = gens[0][x]/float(gen_size*1.1))
    p_frame = line([[-.5,-.5],[-.5,ngens-.5], [gen_size-.5,ngens-.5], [gen_size-.5,-.5], [-.5,-.5]])
    for g in range(1,ngens):
        for x in range(gen_size):
            old_x = inds[g-1][x]
            gen_lines += line([[x,ngens-g-1],[old_x,ngens-g]], hue = gens[g-1][old_x]/float(gen_size*1.1))
            pts += point((x,ngens-g-1), hue = gens[g][x]/float(gen_size*1.1))
    return pts+gen_lines+p_frame
d_field = RealField(10)
@interact
def coalescents(pop_size = slider(2,100,1,15,'Population size'), selection = slider(-1,1,.1,0, 'Selection for first taxon'), s = selector(['Again!'], label='Refresh', buttons=True)):
    print 'Population size: ' + str(pop_size)
    print 'Selection coefficient for first taxon: ' + str(d_field(selection))
    start = [i for i in range(pop_size)]
    gens = [start]
    inds = []
    while gens[-1][0] != gens[-1][-1]:
        g_index = len(gens) - 1
        n_gen = next_gen(gens[g_index], selection = selection)
        gens.append(n_gen[0])
        inds.append(n_gen[1])
        coal_data1 = [gens,inds]
    print 'Generations until coalescence: ' + str(len(gens))
    show(coal_plot(coal_data1), axes = False, figsize = [8,4.0*len(gens)/pop_size], ymax = len(gens)-1)

attachment:coalescent.png

Miscellaneous Graphics

Catalog of 3D Parametric Plots

var('u,v')
plots = ['Two Interlinked Tori', 'Star of David', 'Double Heart',
         'Heart', 'Green bowtie', "Boy's Surface", "Maeder's Owl",
         'Cross cap']
plots.sort()

@interact
def _(example=selector(plots, buttons=True, nrows=2),
      tachyon=("Raytrace", False), frame = ('Frame', False),
      opacity=(1,(0.1,1))):
    url = ''
    if example == 'Two Interlinked Tori':
        f1 = (4+(3+cos(v))*sin(u), 4+(3+cos(v))*cos(u), 4+sin(v))
        f2 = (8+(3+cos(v))*cos(u), 3+sin(v), 4+(3+cos(v))*sin(u))
        p1 = parametric_plot3d(f1, (u,0,2*pi), (v,0,2*pi), color="red", opacity=opacity)
        p2 = parametric_plot3d(f2, (u,0,2*pi), (v,0,2*pi), color="blue",opacity=opacity)
        P = p1 + p2
    elif example == 'Star of David':
        f_x = cos(u)*cos(v)*(abs(cos(3*v/4))^500 + abs(sin(3*v/4))^500)^(-1/260)*(abs(cos(4*u/4))^200 + abs(sin(4*u/4))^200)^(-1/200)
        f_y = cos(u)*sin(v)*(abs(cos(3*v/4))^500 + abs(sin(3*v/4))^500)^(-1/260)*(abs(cos(4*u/4))^200 + abs(sin(4*u/4))^200)^(-1/200)
        f_z = sin(u)*(abs(cos(4*u/4))^200 + abs(sin(4*u/4))^200)^(-1/200)
        P = parametric_plot3d([f_x, f_y, f_z], (u, -pi, pi), (v, 0, 2*pi),opacity=opacity)
    elif example == 'Double Heart':
        f_x = ( abs(v) - abs(u) - abs(tanh((1/sqrt(2))*u)/(1/sqrt(2))) + abs(tanh((1/sqrt(2))*v)/(1/sqrt(2))) )*sin(v)
        f_y = ( abs(v) - abs(u) - abs(tanh((1/sqrt(2))*u)/(1/sqrt(2))) - abs(tanh((1/sqrt(2))*v)/(1/sqrt(2))) )*cos(v)
        f_z = sin(u)*(abs(cos(4*u/4))^1 + abs(sin(4*u/4))^1)^(-1/1)
        P = parametric_plot3d([f_x, f_y, f_z], (u, 0, pi), (v, -pi, pi),opacity=opacity)
    elif example == 'Heart':
        f_x = cos(u)*(4*sqrt(1-v^2)*sin(abs(u))^abs(u))
        f_y = sin(u) *(4*sqrt(1-v^2)*sin(abs(u))^abs(u))
        f_z = v
        P = parametric_plot3d([f_x, f_y, f_z], (u, -pi, pi), (v, -1, 1), frame=False, color="red",opacity=opacity)
    elif example == 'Green bowtie':
        f_x = sin(u) / (sqrt(2) + sin(v))
        f_y = sin(u) / (sqrt(2) + cos(v))
        f_z = cos(u) / (1 + sqrt(2))
        P = parametric_plot3d([f_x, f_y, f_z], (u, -pi, pi), (v, -pi, pi), frame=False, color="green",opacity=opacity)
    elif example == "Boy's Surface":
        url = "http://en.wikipedia.org/wiki/Boy's_surface"
        fx = 2/3* (cos(u)* cos(2*v) + sqrt(2)* sin(u)* cos(v))* cos(u) / (sqrt(2) - sin(2*u)* sin(3*v))
        fy = 2/3* (cos(u)* sin(2*v) - sqrt(2)* sin(u)* sin(v))* cos(u) / (sqrt(2) - sin(2*u)* sin(3*v))
        fz = sqrt(2)* cos(u)* cos(u) / (sqrt(2) - sin(2*u)* sin(3*v))
        P = parametric_plot3d([fx, fy, fz], (u, -2*pi, 2*pi), (v, 0, pi), plot_points = [90,90], frame=False, color="orange",opacity=opacity) 
    elif example == "Maeder's Owl":
        fx = v *cos(u) - 0.5* v^2 * cos(2* u)
        fy = -v *sin(u) - 0.5* v^2 * sin(2* u)
        fz = 4 *v^1.5 * cos(3 *u / 2) / 3
        P = parametric_plot3d([fx, fy, fz], (u, -2*pi, 2*pi), (v, 0, 1),plot_points = [90,90], frame=False, color="purple",opacity=opacity)
    elif example =='Cross cap':
        url = 'http://en.wikipedia.org/wiki/Cross-cap'
        fx = (1+cos(v))*cos(u)
        fy = (1+cos(v))*sin(u)
        fz = -tanh((2/3)*(u-pi))*sin(v)
        P = parametric_plot3d([fx, fy, fz], (u, 0, 2*pi), (v, 0, 2*pi), frame=False, color="red",opacity=opacity)
    else:
        print "Bug selecting plot?"
        return


    html('<h2>%s</h2>'%example)
    if url:
        html('<h3><a target="_new" href="%s">%s</a></h3>'%(url,url))
    show(P, viewer='tachyon' if tachyon else 'jmol', frame=frame)

attachment:parametricplot3d.png

Interactive rotatable raytracing with Tachyon3d

C = cube(color=['red', 'green', 'blue'], aspect_ratio=[1,1,1],
         viewer='tachyon') + sphere((1,0,0),0.2)
@interact
def example(theta=(0,2*pi), phi=(0,2*pi), zoom=(1,(1,4))):
    show(C.rotate((0,0,1), theta).rotate((0,1,0),phi), zoom=zoom)

attachment:tachyonrotate.png

Interactive 3d plotting

var('x,y')
@interact
def example(clr=Color('orange'), f=4*x*exp(-x^2-y^2), xrange='(-2, 2)', yrange='(-2,2)', 
    zrot=(0,pi), xrot=(0,pi), zoom=(1,(1/2,3)), square_aspect=('Square Frame', False),
    tachyon=('Ray Tracer', True)):
    xmin, xmax = sage_eval(xrange); ymin, ymax = sage_eval(yrange)
    P = plot3d(f, (x, xmin, xmax), (y, ymin, ymax), color=clr)
    html('<h1>Plot of $f(x,y) = %s$</h1>'%latex(f))
    aspect_ratio = [1,1,1] if square_aspect else [1,1,1/2]
    show(P.rotate((0,0,1), -zrot).rotate((1,0,0),xrot), 
         viewer='tachyon' if tachyon else 'jmol', 
         figsize=6, zoom=zoom, frame=False,
         frame_aspect_ratio=aspect_ratio)

attachment:tachyonplot3d.png

Anchor(eggpaint)

Somewhat Silly Egg Painter

by Marshall Hampton (refereed by William Stein)

var('s,t')
g(s) = ((0.57496*sqrt(121 - 16.0*s^2))/sqrt(10.+ s))
def P(color, rng):
    return parametric_plot3d((cos(t)*g(s), sin(t)*g(s), s), (s,rng[0],rng[1]), (t,0,2*pi), plot_points = [150,150], rgbcolor=color, frame = False, opacity = 1)
colorlist = ['red','blue','red','blue']
@interact
def _(band_number = selector(range(1,5)), current_color = Color('red')):
    html('<h1 align=center>Egg Painter</h1>')
    colorlist[band_number-1] = current_color
    egg = sum([P(colorlist[i],[-2.75+5.5*(i/4),-2.75+5.5*(i+1)/4]) for i in range(4)])
    show(egg)

attachment:eggpaint.png