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| = Sage Interactions = | #Choose the size D of the square matrix: D = 3 |
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| 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 sage-support@googlegroups.com. * [:interact/graph_theory:Graph Theory] * [:interact/calculus:Calculus] * [:interact/diffeq:Differential Equations] * [:interact/linear_algebra:Linear Algebra] * [:interact/algebra:Algebra] * [:interact/number_theory:Number Theory] * [:interact/web:Web Applications] == 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() |
example = [[1 if k==j else 0 for k in range(D)] for j in range(D)] example[0][-1] = 2 example[-1][0] = 3 |
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| 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?" |
def _(M=input_grid(D,D, default = example, label='Matrix to invert', to_value=matrix), tt = text_control('Enter the bits of precision used' ' (only if you entered floating point numbers)'), precision = slider(5,100,5,20), auto_update=False): if det(M)==0: print 'Failure: Matrix is not invertible' |
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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 == Miscellaneous == == Profile a snippet of code == {{{ html('<h2>Profile the given input</h2>') import cProfile; import profile @interact def _(cmd = ("Statement", '2 + 2'), do_preparse=("Preparse?", True), cprof =("cProfile?", False)): if do_preparse: cmd = preparse(cmd) print "<html>" # trick to avoid word wrap if cprof: cProfile.run(cmd) else: profile.run(cmd) print "</html>" }}} attachment:profile.png === Evaluate a bit of code in a given system === by William Stein (there is no way yet to make the text box big): {{{ @interact def _(system=selector([('sage0', 'Sage'), ('gp', 'PARI'), ('magma', 'Magma')]), code='2+2'): print globals()[system].eval(code) }}} attachment:evalsys.png === A Random Walk === by William Stein {{{ html('<h1>A Random Walk</h1>') vv = []; nn = 0 @interact def foo(pts = checkbox(True, "Show points"), refresh = checkbox(False, "New random walk every time"), steps = (50,(10..500))): # We cache the walk in the global variable vv, so that # checking or unchecking the points checkbox doesn't change # the random walk. html("<h2>%s steps</h2>"%steps) global vv if refresh or len(vv) == 0: s = 0; v = [(0,0)] for i in range(steps): s += random() - 0.5 v.append((i, s)) vv = v elif len(vv) != steps: # Add or subtract some points s = vv[-1][1]; j = len(vv) for i in range(steps - len(vv)): s += random() - 0.5 vv.append((i+j,s)) v = vv[:steps] else: v = vv L = line(v, rgbcolor='#4a8de2') if pts: L += points(v, pointsize=10, rgbcolor='red') show(L, xmin=0, figsize=[8,3]) }}} attachment:randomwalk.png === 3D Random Walk === {{{ @interact def rwalk3d(n=(50,1000), frame=True): pnt = [0,0,0] v = [copy(pnt)] for i in range(n): pnt[0] += random()-0.5 pnt[1] += random()-0.5 pnt[2] += random()-0.5 v.append(copy(pnt)) show(line3d(v,color='black'),aspect_ratio=[1,1,1],frame=frame) }}} attachment:randomwalk3d.png |
if M.base_ring() == RR: M = M.apply_map(RealField(precision)) N=M M=M.augment(identity_matrix(D)) print 'We construct the augmented matrix' show(M) for m in range(0,D-1): if M[m,m] == 0: lista = [(M[j,m],j) for j in range(m,D)] maxi, c = max(lista) M[c,:],M[m,:]=M[m,:],M[c,:] print 'We permute rows %d and %d'%(m+1,c+1) show(M) for n in range(m+1,D): a=M[m,m] if M[n,m]!=0: print "We add %s times row %d to row %d"%(-M[n,m]/a, m+1, n+1) M=M.with_added_multiple_of_row(n,m,-M[n,m]/a) show(M) for m in range(D-1,-1,-1): for n in range(m-1,-1,-1): a=M[m,m] if M[n,m]!=0: print "We add %s times row %d to the row %d"%(-M[n,m]/a, m+1, n+1) M=M.with_added_multiple_of_row(n,m,-M[n,m]/a) show(M) for m in range(0,D): if M[m,m]!=1: print 'We divide row %d by %s'%(m+1,M[m,m]) M = M.with_row_set_to_multiple_of_row(m,m,1/M[m,m]) show(M) M=M.submatrix(0,D,D) print 'We keep the right submatrix, which contains the inverse' html('$$M^{-1}=%s$$'%latex(M)) print 'We check it actually is the inverse' html('$$M^{-1}*M=%s*%s=%s$$'%(latex(M),latex(N),latex(M*N))) |
D = 3
example = [[1 if k==j else 0 for k in range(D)] for j in range(D)] example[0][-1] = 2 example[-1][0] = 3
@interact def _(M=input_grid(D,D, default = example,
- label='Matrix to invert', to_value=matrix),
- tt = text_control('Enter the bits of precision used'
- ' (only if you entered floating point numbers)'),
- if det(M)==0:
- print 'Failure: Matrix is not invertible' return
M = M.apply_map(RealField(precision))
- if M[m,m] == 0:
- lista = [(M[j,m],j) for j in range(m,D)] maxi, c = max(lista) M[c,:],M[m,:]=M[m,:],M[c,:] print 'We permute rows %d and %d'%(m+1,c+1) show(M)
- a=M[m,m] if M[n,m]!=0:
- print "We add %s times row %d to row %d"%(-M[n,m]/a, m+1, n+1) M=M.with_added_multiple_of_row(n,m,-M[n,m]/a) show(M)
- for n in range(m-1,-1,-1):
- a=M[m,m] if M[n,m]!=0:
- print "We add %s times row %d to the row %d"%(-M[n,m]/a, m+1, n+1) M=M.with_added_multiple_of_row(n,m,-M[n,m]/a) show(M)
- a=M[m,m] if M[n,m]!=0:
- if M[m,m]!=1:
- print 'We divide row %d by %s'%(m+1,M[m,m]) M = M.with_row_set_to_multiple_of_row(m,m,1/M[m,m]) show(M)
html('
M^{-1}=%s'%latex(M)) print 'We check it actually is the inverse' html('M^{-1}*M=%s*%s=%s'%(latex(M),latex(N),latex(M*N)))