def BM_histogram(n=20, runs=100, **kwargs):
plotter.Plotter.show_plots = False
logger.VERBOSE = False
Model = models.BooleanModel
pbar = ProgressBar(maxval=runs)
all_data = []
pbar.start()
for i in range(runs):
e_num = round(n * 2.33)
act = round(2133/(2133+1768) * e_num)
inh = e_num-act
#print(n, e_num, act, inh)
g = utils.GraphGenerator.get_random_graph(n, activating_edges=act, inhibiting_edges=inh)
sim = g.system.simulate(Model, **kwargs)
all_data.extend(sim.flatten())
pbar.update(i)
pbar.finish()
plt.gca().set_xscale('log')
plt.gca().set_yscale('log')
utils.present(
'Histogram of simulated gene expression vector (%s, %s)' % (Model.info['name'], 'time norm' if models.BooleanModel.info['norm_time'] else 'gene norm'), plotter.Plotter.plot_histogram,
'gene concentration', 'count', all_data,
bins=np.logspace(-4, 0, 200)
)
def main():
vol, top = load_data()
downsample = 3
fig = mlab.figure(bgcolor=(1,1,1))
x, y, z = hor2xyz(top, vol, downsample)
build_sides(vol, x, y, z, vol.nz)
# Build top
seafloor = top_texture(top, vol)
top_mesh = mlab.mesh(x, y, z)
texture(top_mesh, np.flipud(seafloor.T), cm.gray)
build_base(x, y, z, vol)
utils.present(fig)
def main():
z, x, y = read('data/alaska/clipped_elev.tif')
rgb, _, _ = read('data/alaska/clipped_map.tif')
rgb = np.swapaxes(rgb.T, 0, 1)
fig = mlab.figure()
surf = mlab.mesh(x[::2, ::2], y[::2, ::2], z[::2, ::2])
utils.texture(surf, rgb)
build_sides(x, y, z, -1000)
build_bottom(x, y, z, -1000)
utils.scale(fig, (1, 1, 2.5))
utils.scale(fig, 0.00001)
# shapeways_io.save_vrml(fig, 'models/alaska_textured_sides.zip')
utils.present(fig)
def main():
vol, coh, base, top = load_data()
downsample = 3
_, _, zbase = hor2xyz(base, vol, downsample)
x, y, ztop = hor2xyz(top, vol, downsample)
fig = mlab.figure(bgcolor=(1,1,1))
build_sides(vol, x, y, ztop, zbase.min(), zbase)
# Build Base
base_mesh = mlab.mesh(x, y, zbase)
chan = bottom_texture(base, vol)
texture(base_mesh, np.flipud(chan.T), cm.gray)
# Build top
x, y, ztop = hor2xyz(top, vol, downsample)
seafloor = top_texture(top, coh)
top_mesh = mlab.mesh(x, y, ztop)
texture(top_mesh, np.flipud(seafloor.T), cm.gray)
utils.present(fig)
The boy surface is a mathematical parametric surface, see http://en.wikipedia.org/wiki/Boy%27s_surface . We display it by sampling the two parameters of the surface on a grid and using the mlab's mesh function: :func:`mayavi.mlab.mesh`. """ # Author: Gael Varoquaux <*****@*****.**> # Copyright (c) 2007, Enthought, Inc. # License: BSD Style. from numpy import sin, cos, mgrid, pi, sqrt from mayavi import mlab import utils fig = mlab.figure(fgcolor=(0, 0, 0), bgcolor=(1, 1, 1)) u, v = mgrid[-0.035:pi:0.01, -0.035:pi:0.01] X = 2 / 3.0 * (cos(u) * cos(2 * v) + sqrt(2) * sin(u) * cos(v)) * cos(u) / (sqrt(2) - sin(2 * u) * sin(3 * v)) Y = 2 / 3.0 * (cos(u) * sin(2 * v) - sqrt(2) * sin(u) * sin(v)) * cos(u) / (sqrt(2) - sin(2 * u) * sin(3 * v)) Z = -sqrt(2) * cos(u) * cos(u) / (sqrt(2) - sin(2 * u) * sin(3 * v)) S = sin(u) mlab.mesh(X, Y, Z, scalars=S, colormap="YlGnBu") # Nice view from the front mlab.view(0.0, -5.0, 4) utils.present(fig)