def display(self,bgcolor=None,showAxes=False):
mlab.figure(bgcolor=bgcolor)
for x,y,z,op,col in zip(self.xMesh,self.yMesh,self.zMesh,self.meshOpacity,self.meshColor):
mlab.mesh(x,y,z,opacity=op,color=col)
if showAxes:
mlab.axes()
mlab.show()
def plot_mayavi(self):
"""Use mayavi to plot a phenotype phase plane in 3D.
The resulting figure will be quick to interact with in real time,
but might be difficult to save as a vector figure.
returns: mlab figure object"""
from mayavi import mlab
figure = mlab.figure(bgcolor=(1, 1, 1), fgcolor=(0, 0, 0))
figure.name = "Phenotype Phase Plane"
max = 10.0
xmax = self.reaction1_fluxes.max()
ymax = self.reaction2_fluxes.max()
zmax = self.growth_rates.max()
xgrid, ygrid = meshgrid(self.reaction1_fluxes, self.reaction2_fluxes)
xgrid = xgrid.transpose()
ygrid = ygrid.transpose()
xscale = max / xmax
yscale = max / ymax
zscale = max / zmax
mlab.surf(xgrid * xscale, ygrid * yscale, self.growth_rates * zscale,
representation="wireframe", color=(0, 0, 0), figure=figure)
mlab.mesh(xgrid * xscale, ygrid * yscale, self.growth_rates * zscale,
scalars=self.shadow_prices1 + self.shadow_prices2,
resolution=1, representation="surface", opacity=0.75,
figure=figure)
# draw axes
mlab.outline(extent=(0, max, 0, max, 0, max))
mlab.axes(opacity=0, ranges=[0, xmax, 0, ymax, 0, zmax])
mlab.xlabel(self.reaction1_name)
mlab.ylabel(self.reaction2_name)
mlab.zlabel("Growth rates")
return figure
def draw_working_area(self, width, height):
color = (0.9, 0.9, 0.7)
x, y = np.mgrid[0:height+1:10, 0:width+1:10]
z = np.zeros(x.shape)
mlab.surf(x, y, z, color=color, line_width=1.0,
representation='wireframe', warp_scale=self.scale)
mlab.axes()
def labels(self): ''' Add 3d text to show the axes. ''' fontsize = max(self.xrang, self.yrang)/40. tcolor = (1,1,1) mlab.text3d(self.xrang/2,-40,self.zrang+40,'R.A.',scale=fontsize,orient_to_camera=True,color=tcolor) mlab.text3d(-40,self.yrang/2,self.zrang+40,'Decl.',scale=fontsize,orient_to_camera=True,color=tcolor) mlab.text3d(-40,-40,self.zrang/2-10,'V (km/s)',scale=fontsize,orient_to_camera=True,color=tcolor) # Label the coordinates of the corners # Lower left corner ra0 = self.extent[0]; dec0 = self.extent[2] c = coord.ICRS(ra=ra0, dec=dec0, unit=(u.degree, u.degree)) RA_ll = str(int(c.ra.hms.h))+'h'+str(int(c.ra.hms.m))+'m'+str(round(c.ra.hms.s,1))+'s' mlab.text3d(0,-20,self.zrang+20,RA_ll,scale=fontsize,orient_to_camera=True,color=tcolor) DEC_ll = str(int(c.dec.dms.d))+'d'+str(int(abs(c.dec.dms.m)))+'m'+str(round(abs(c.dec.dms.s),1))+'s' mlab.text3d(-80,0,self.zrang+20,DEC_ll,scale=fontsize,orient_to_camera=True,color=tcolor) # Upper right corner ra0 = self.extent[1]; dec0 = self.extent[3] c = coord.ICRS(ra=ra0, dec=dec0, unit=(u.degree, u.degree)) RA_ll = str(int(c.ra.hms.h))+'h'+str(int(c.ra.hms.m))+'m'+str(round(c.ra.hms.s,1))+'s' mlab.text3d(self.xrang,-20,self.zrang+20,RA_ll,scale=fontsize,orient_to_camera=True,color=tcolor) DEC_ll = str(int(c.dec.dms.d))+'d'+str(int(abs(c.dec.dms.m)))+'m'+str(round(abs(c.dec.dms.s),1))+'s' mlab.text3d(-80,self.yrang,self.zrang+20,DEC_ll,scale=fontsize,orient_to_camera=True,color=tcolor) # V axis if self.extent[5] > self.extent[4]: v0 = self.extent[4]; v1 = self.extent[5] else: v0 = self.extent[5]; v1 = self.extent[4] mlab.text3d(-20,-20,self.zrang,str(round(v0,1)),scale=fontsize,orient_to_camera=True,color=tcolor) mlab.text3d(-20,-20,0,str(round(v1,1)),scale=fontsize,orient_to_camera=True,color=tcolor) mlab.axes(self.field, ranges=self.extent, x_axis_visibility=False, y_axis_visibility=False, z_axis_visibility=False) mlab.outline()
def plotDensity(mToB,coeffs,n=100,plotVals="real",plotBnd=True):
"""Plot boundary density with Mayavi
INPUT:
mToB - Mesh-to-Basis map
coeffs - Coefficients of boundary density
n - Discretisation points per element (default 100)
plotVals - "real", "imag" or "abs" for real/imaginary part or absolute values
(default "real")
plotBnd - Also plot boundary of shape (default True)
"""
from mayavi import mlab
transforms={"real":numpy.real,"imag":numpy.imag,"abs":numpy.abs}
x,f=evalDensity(mToB,coeffs,n)
f=transforms[plotVals](f)
xmin=min(x[0])
xmax=max(x[0])
ymin=min(x[1])
ymax=max(x[1])
zmin=max([-1,min(f)])
zmax=min([1,max(f)])
extent=[xmin,xmax,ymin,ymax,zmin,zmax]
ranges=[xmin,xmax,ymin,ymax,min(f),max(f)]
fig=mlab.figure(bgcolor=(1,1,1))
mlab.plot3d(x[0],x[1],f,extent=extent,color=(0,0,0),tube_radius=None,figure=fig)
if plotBnd:
mlab.plot3d(x[0],x[1],numpy.zeros(x[0].shape),extent=[xmin,xmax,ymin,ymax,0,0],tube_radius=None,figure=fig)
mlab.axes(extent=extent,ranges=ranges,line_width=3.0,figure=fig)
mlab.show()
def action(u, x, xv, y, yv, t, n):
#print 'action, t=',t,'\nu=',u, '\Nx=',x, '\Ny=', y
if plot == 1:
mesh(xv, yv, u, title='t=%g' %t[n])
time.sleep(0.2) # pause between frames
elif plot == 2:
# mayavi plotting
mlab.clf()
extent1 = (0, 20, 0, 20,-2, 2)
s = mlab.surf(x , y, u, colormap='Blues', warp_scale=5,extent=extent1)
mlab.axes(s, color=(.7, .7, .7), extent=extent1,
ranges=(0, 10, 0, 10, -1, 1), xlabel='', ylabel='',
zlabel='',
x_axis_visibility=False, z_axis_visibility=False)
mlab.outline(s, color=(0.7, .7, .7), extent=extent1)
mlab.text(2, -2.5, '', z=-4, width=0.1)
mlab.colorbar(object=None, title=None, orientation='horizontal', nb_labels=None, nb_colors=None, label_fmt=None)
mlab.title('test 1D t=%g' % t[n])
mlab.view(142, -72, 50)
f = mlab.gcf()
camera = f.scene.camera
camera.yaw(0)
if plot > 0:
path = 'Figures_wave2D'
time.sleep(0) # pause between frames
if save_plot and plot != 2:
filename = '%s/%08d.png' % (path, n)
savefig(filename) # time consuming!
elif save_plot and plot == 2:
filename = '%s/%08d.png' % (path,n)
mlab.savefig(filename) # time consuming!
def animateGIF(filename, prices):
'''Creates a mayavi visualization of a pd DataFrame containing stock prices
Then uses MoviePy to animate and save as a gif
Inputs:
prices => a pd DataFrame, w/ index: dates; columns: company names
'''
#Because of mayavi requirements, replace dates and company names with integers
#until workaround is figured out
x_length, y_length = prices.shape
xTime = np.array([list(xrange(x_length)),] * y_length).transpose()
yCompanies = np.array([list(xrange(y_length)),] * x_length)
#Sort indexed prices by total return on last date
lastDatePrices = prices.iloc[-1]
lastDatePrices.sort_values(inplace=True)
sortOrder = lastDatePrices.index
zPrices = prices[sortOrder]
#Create mayavi2 object
dims = xTime.shape
fig = mlab.figure(bgcolor=(.4,.4,.4))
vis = mlab.surf(xTime, yCompanies, zPrices)
mlab.outline(vis)
mlab.orientation_axes(vis)
mlab.axes(vis, nb_labels=0, xlabel = 'Time', ylabel = 'Company', zlabel = 'Price')
# duration = 2 #Duration of the animation in seconds (will loop)
animation = mpy.VideoClip(make_frame, duration = 4).resize(1.0)
# animation.write_videofile('prototype_animation.mp4', fps=20)
animation.write_gif(filename, fps=20)
def show_sensors(pth, red=None, green=None):
"""
show sensors stored in a h5.
:param red: a list of labels to be shown in red
"""
if red is None:
red = []
if green is None:
green = []
mlab.figure()
sensors = h5py.File(pth)
d = numpy.array(sensors['locations'])
labels = list(sensors['labels'])
highlight = numpy.ones(d.shape[0])
for i, l in enumerate(labels):
if l in red:
highlight[i] = 5.0
elif l in green:
highlight[i] = 7.0
else:
highlight[i] = 2.0
mlab.points3d(d[:,0], d[:,1], d[:,2], highlight, scale_mode='none')
mlab.axes()
def visualizePrices(prices):
'''Creates a mayavi visualization of a pd DataFrame containing stock prices
Inputs:
prices => a pd DataFrame, w/ index: dates; columns: company names
'''
#Imports mlab here to delay starting of mayavi engine until necessary
from mayavi import mlab
#Because of current mayavi requirements, replaces dates and company names with integers
x_length, y_length = prices.shape
xTime = np.array([list(xrange(x_length)),] * y_length).transpose()
yCompanies = np.array([list(xrange(y_length)),] * x_length)
#Sort indexed prices by total return on last date
lastDatePrices = prices.iloc[-1]
lastDatePrices.sort_values(inplace=True)
sortOrder = lastDatePrices.index
zPrices = prices[sortOrder]
#Create mayavi2 object
fig = mlab.figure(bgcolor=(.4,.4,.4))
vis = mlab.surf(xTime, yCompanies, zPrices)
mlab.outline(vis)
mlab.orientation_axes(vis)
#mlab.title('S&P 500 Market Data Visualization', size = .25)
mlab.axes(vis, nb_labels=0, xlabel = 'Time', ylabel = 'Company', zlabel = 'Price')
mlab.show()
def plot3D(name, X, Y, Z, zlabel):
"""
Plots a 3d surface plot of Z using the mayavi mlab.mesh function.
Parameters
----------
name: string
The name of the figure.
X: 2d ndarray
The x-axis data.
Y: 2d ndarray
The y-axis data.
Z: 2d nd array
The z-axis data.
zlabel: The title that appears on the z-axis.
"""
mlab.figure(name)
mlab.clf()
plotData = mlab.mesh(X/(np.max(X) - np.min(X)),
Y/(np.max(Y) - np.min(Y)),
Z/(np.max(Z) - np.min(Z)))
mlab.outline(plotData)
mlab.axes(plotData, ranges=[np.min(X), np.max(X),
np.min(Y), np.max(Y),
np.min(Z), np.max(Z)])
mlab.xlabel('Space ($x$)')
mlab.ylabel('Time ($t$)')
mlab.zlabel(zlabel)
def plot_mcontour(self, ndim0, ndim1, z, show_mode):
"use mayavi.mlab to plot contour."
if not mayavi_installed:
self.__logger.info("Mayavi is not installed on your device.")
return
#do 2d interpolation
#get slice object
s = np.s_[0:ndim0:1, 0:ndim1:1]
x, y = np.ogrid[s]
mx, my = np.mgrid[s]
#use cubic 2d interpolation
interpfunc = interp2d(x, y, z, kind='cubic')
newx = np.linspace(0, ndim0, 600)
newy = np.linspace(0, ndim1, 600)
newz = interpfunc(newx, newy)
#mlab
face = mlab.surf(newx, newy, newz, warp_scale=2)
mlab.axes(xlabel='x', ylabel='y', zlabel='z')
mlab.outline(face)
#save or show
if show_mode == 'show':
mlab.show()
elif show_mode == 'save':
mlab.savefig('mlab_contour3d.png')
else:
raise ValueError('Unrecognized show mode parameter : ' +
show_mode)
return
def plot(self):
"""Plots the geometry using the package Mayavi."""
print('\nPlot the three-dimensional geometry ...')
from mayavi import mlab
x_init = self.gather_coordinate('x', position='initial')
y_init = self.gather_coordinate('y', position='initial')
z_init = self.gather_coordinate('z', position='initial')
x = self.gather_coordinate('x')
y = self.gather_coordinate('y')
z = self.gather_coordinate('z')
figure = mlab.figure('body', size=(600, 600))
figure.scene.disable_render = False
same = (numpy.allclose(x, x_init, rtol=1.0E-06) and
numpy.allclose(y, y_init, rtol=1.0E-06) and
numpy.allclose(z, z_init, rtol=1.0E-06))
if not same:
mlab.points3d(x_init, y_init, z_init, name='initial',
scale_factor=0.01, color=(0, 0, 1))
mlab.points3d(x, y, z, name='current',
scale_factor=0.01, color=(1, 0, 0))
mlab.axes()
mlab.orientation_axes()
mlab.outline()
figure.scene.disable_render = True
mlab.show()
def AortaSinusoidModelingVisualization(filename):
path = 'C:\\Users\\shijingliu\\Dropbox\\Reggie\\Results\\Sinusoid Modeling Result (2 seconds window size)\\Aorta Modeling Results\\'
file = filename
finalname = path+file+'.csv'
'declare the x, y, z, s array for point visualization'
index = 0
x_array = []
y_array = []
z_array = []
s_array = []
with open(finalname, 'rb') as csvfile:
rowreader = csv.reader(csvfile)
for row in rowreader:
if index <1:
index = index + 1
else:
s = int(row[0])
x_data = float(row[1])
y_data = float(row[2])
z_data = float(row[3])
if (np.abs(x_data)<=20.0) and (np.abs(y_data)<=20.0) and (np.abs(z_data)<=200.0):
s_array.append(s)
x_array.append(x_data)
y_array.append(y_data)
z_array.append(z_data)
mlab.axes(mlab.outline(mlab.points3d(x_array, y_array, z_array, s_array, colormap="Reds", scale_mode='none')))
def PlotHorizon3d(tss):
"""
Plot a list of horizons.
Parameters
----------
tss : list of trappedsurface
All the trapped surfaces to visualize.
"""
from mayavi import mlab
cmaps = ['bone', 'jet', 'hot', 'cool', 'spring', 'summer', 'winter']
assert len(cmaps) > len(tss)
extents = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
for ts, cm in zip(tss, cmaps):
mlab.mesh(ts.X, ts.Y, ts.Z, colormap=cm, opacity=0.4)
extents[0] = min(extents[0], np.min(ts.X))
extents[1] = max(extents[1], np.max(ts.X))
extents[2] = min(extents[2], np.min(ts.Y))
extents[3] = max(extents[3], np.max(ts.Y))
extents[4] = min(extents[4], np.min(ts.Z))
extents[5] = max(extents[5], np.max(ts.Z))
mlab.axes(extent=extents)
mlab.outline(extent=extents)
mlab.show()
def animateGIF(filename, prices):
'''Creates a mayavi visualization of a pd DataFrame containing stock prices
Then uses MoviePy to animate and save as a gif
Inputs:
prices => a pd DataFrame, w/ index: dates; columns: company names
'''
#Imports mlab here to delay starting of mayavi engine until necessary
from mayavi import mlab
#Because of current mayavi requirements, replaces dates and company names with integers
x_length, y_length = prices.shape
xTime = np.array([list(xrange(x_length)),] * y_length).transpose()
yCompanies = np.array([list(xrange(y_length)),] * x_length)
#Sort indexed prices by total return on last date
lastDatePrices = prices.iloc[-1]
lastDatePrices.sort_values(inplace=True)
sortOrder = lastDatePrices.index
zPrices = prices[sortOrder]
#Create mayavi2 object
fig = mlab.figure(bgcolor=(.4,.4,.4))
vis = mlab.surf(xTime, yCompanies, zPrices)
mlab.outline(vis)
mlab.orientation_axes(vis)
mlab.axes(vis, nb_labels=0, xlabel = 'Time', ylabel = 'Company', zlabel = 'Price')
animation = mpy.VideoClip(make_frame, duration = 4).resize(1.0)
animation.write_gif(filename, fps=20)
def visualizePrices(prices):
'''Creates a mayavi visualization of a pd DataFrame containing stock prices
Inputs:
prices => a pd DataFrame, w/ index: dates; columns: company names
'''
#Because of mayavi requirements, replace dates and company names with integers
#until workaround is figured out
x_length, y_length = prices.shape
xTime = np.array([list(xrange(x_length)),] * y_length).transpose()
yCompanies = np.array([list(xrange(y_length)),] * x_length)
#Sort indexed prices by total return on last date
lastDatePrices = prices.iloc[-1]
lastDatePrices.sort_values(inplace=True)
sortOrder = lastDatePrices.index
zPrices = prices[sortOrder]
#Create mayavi2 object
dims = xTime.shape
fig = mlab.figure(bgcolor=(.4,.4,.4))
vis = mlab.surf(xTime, yCompanies, zPrices)
mlab.outline(vis)
mlab.orientation_axes(vis)
#mlab.title('S&P 500 Market Data Visualization', size = .25)
mlab.axes(vis, nb_labels=0, xlabel = 'Time', ylabel = 'Company', zlabel = 'Price')
#Functionality to be added:
# cursor3d = mlab.points3d(0., 0., 0., mode='axes',
# color=(0, 0, 0),
# scale_factor=20)
#picker = fig.on_mouse_pick(picker_callback)
mlab.show()
def etsIntro():
x, y = np.ogrid[-2:2:20j, -2:2:20j]
z = x * np.exp( - x**2 - y**2)
pl = mlab.surf(x, y, z, warp_scale="auto")
mlab.axes(xlabel='x', ylabel='y', zlabel='z')
mlab.outline(pl)
def plot_3D_spectrum(self, xmin=None, xmax=None, xN=None, ymin=None,
ymax=None, yN=None, trajectory=False, tube_radius=1e-2,
part='imag'):
"""Plot the Riemann sheet structure around the EP.
Parameters:
-----------
xmin, xmax: float
Dimensions in x-direction.
ymin, ymax: float
Dimensions in y-direction.
xN, yN: int
Number of sampling points in x and y direction.
trajectory: bool
Whether to include a projected trajectory of the eigenbasis
coefficients.
part: str
Which function to apply to the eigenvalues before plotting.
tube_radius: float
Trajectory tube thickness.
"""
from mayavi import mlab
X, Y, Z = self.sample_H(xmin, xmax, xN, ymin, ymax, yN)
Z0, Z1 = [Z[..., n] for n in (0, 1)]
def get_min_and_max(*args):
data = np.concatenate(*args)
return data.min(), data.max()
surf_kwargs = dict(colormap='Spectral', mask=np.diff(Z0.real) > 0.015)
mlab.figure(0)
Z_min, Z_max = get_min_and_max([Z0.real, Z1.real])
mlab.surf(X.real, Y.real, Z0.real, vmin=Z_min, vmax=Z_max, **surf_kwargs)
mlab.surf(X.real, Y.real, Z1.real, vmin=Z_min, vmax=Z_max, **surf_kwargs)
mlab.axes(zlabel="Re(E)")
mlab.figure(1)
Z_min, Z_max = get_min_and_max([Z0.imag, Z1.imag])
mlab.mesh(X.real, Y.real, Z0.imag, vmin=Z_min, vmax=Z_max, **surf_kwargs)
mlab.mesh(X.real, Y.real, Z1.imag, vmin=Z_min, vmax=Z_max, **surf_kwargs)
mlab.axes(zlabel="Im(E)")
if trajectory:
x, y = self.get_cycle_parameters(self.t)
_, c1, c2 = self.solve_ODE()
for i, part in enumerate([np.real, np.imag]):
e1, e2 = [part(self.eVals[:, n]) for n in (0, 1)]
z = map_trajectory(c1, c2, e1, e2)
mlab.figure(i)
mlab.plot3d(x, y, z, tube_radius=tube_radius)
mlab.points3d(x[0], y[0], z[0],
# color=line_color,
scale_factor=1e-1,
mode='sphere')
mlab.show()
def draw_cloud(self, points3d, scale=1):
scale = self.scale * scale
mlab.points3d(points3d[:, 0], points3d[:, 1],
points3d[:, 2], points3d[:, 2],
colormap='jet', opacity=0.75, scale_factor=scale)
mlab.outline()
mlab.colorbar(title='Planar disparity (mm)')
mlab.axes()
def plot_3d_mayavi(X, Y, Z):
f = figure(bgcolor=(1, 1, 1))
surf(X.T, Y.T, Z, figure=f, warp_scale='auto')
axes(xlabel='N Samples', ylabel='Sample', zlabel='Gradient',
z_axis_visibility=False, nb_labels=10, line_width=1)
show()
def plot_u(u, x, xv, y, yv, t, n):
"""User action function for plotting."""
if t[n] == 0:
time.sleep(2)
if plot_method == 1:
# Works well with Gnuplot backend, not with Matplotlib
st.mesh(x, y, u, title='t=%g' % t[n], zlim=[-1,1],
caxis=[-1,1])
elif plot_method == 2:
# Works well with Gnuplot backend, not with Matplotlib
st.surfc(xv, yv, u, title='t=%g' % t[n], zlim=[-1, 1],
colorbar=True, colormap=st.hot(), caxis=[-1,1],
shading='flat')
elif plot_method == 3:
print 'Experimental 3D matplotlib...under development...'
# Probably too slow
#plt.clf()
ax = fig.add_subplot(111, projection='3d')
u_surf = ax.plot_surface(xv, yv, u, alpha=0.3)
#ax.contourf(xv, yv, u, zdir='z', offset=-100, cmap=cm.coolwarm)
#ax.set_zlim(-1, 1)
# Remove old surface before drawing
if u_surf is not None:
ax.collections.remove(u_surf)
plt.draw()
time.sleep(1)
elif plot_method == 4:
# Mayavi visualization
mlab.clf()
extent1 = (0, 20, 0, 20,-2, 2)
s = mlab.surf(x , y, u,
colormap='Blues',
warp_scale=5,extent=extent1)
mlab.axes(s, color=(.7, .7, .7), extent=extent1,
ranges=(0, 10, 0, 10, -1, 1),
xlabel='', ylabel='', zlabel='',
x_axis_visibility=False,
z_axis_visibility=False)
mlab.outline(s, color=(0.7, .7, .7), extent=extent1)
mlab.text(6, -2.5, '', z=-4, width=0.14)
mlab.colorbar(object=None, title=None,
orientation='horizontal',
nb_labels=None, nb_colors=None,
label_fmt=None)
mlab.title('Gaussian t=%g' % t[n])
mlab.view(142, -72, 50)
f = mlab.gcf()
camera = f.scene.camera
camera.yaw(0)
if plot_method > 0:
time.sleep(0) # pause between frames
if save_plot:
filename = 'tmp_%04d.png' % n
if plot_method == 4:
mlab.savefig(filename) # time consuming!
elif plot_method in (1,2):
st.savefig(filename) # time consuming!
def plotFancy(a):
src = mlab.pipeline.scalar_field(a)
mlab.pipeline.iso_surface(src, contours=[a.min() + 0.1 * a.ptp(), ], opacity=0.1)
mlab.pipeline.iso_surface(src, contours=[a.max() - 0.1 * a.ptp(), ],)
mlab.pipeline.image_plane_widget(src,
plane_orientation='z_axes',
slice_index=len(a[0,0,:])/2,
)
mlab.axes(xlabel="x", ylabel="y", zlabel="z")
def plot(view="iso"):
redis = Redis()
px, py, pz = (redis.get('x'), redis.get('y'), redis.get('z'))
if None in (px, py, pz):
raise UntrainedException("You must train first!")
x, y, z = (pickle.loads(px), pickle.loads(py), pickle.loads(pz))
fig = mlab.figure(size=(800, 600))
# these options could help on certain platforms
# mlab.options.offscreen = True
# fig.scene.off_screen_rendering = True
# Define the points in 3D space
# including color code based on Z coordinate.
mlab.points3d(x, y, z, y)
xlabel = "day of week"
ylabel = "# logins"
zlabel = "hour"
mlab.axes(xlabel=xlabel, ylabel=ylabel, zlabel=zlabel,
ranges=[0, 6, min(y), max(y), 0, 23])
mlab.scalarbar(title=ylabel, nb_labels=10, orientation='vertical')
mlab.orientation_axes(xlabel=xlabel, ylabel=ylabel, zlabel=zlabel)
views = {"xp": fig.scene.x_plus_view,
"xm": fig.scene.x_minus_view,
"yp": fig.scene.y_plus_view,
"ym": fig.scene.y_minus_view,
"zp": fig.scene.z_plus_view,
"zm": fig.scene.z_minus_view,
"iso": fig.scene.isometric_view
}
try:
views[view]()
except KeyError as e:
raise PlotException("Invalid view option: %s" % view)
# can't save directly to stringIO, so have to go through a file
fig.scene.save_png('fig.png')
# mayavi doesn't seem to play well with celery on some platforms and
# doesn't shut down properly - probably because it's in a background thread
# on centos, celery just throws a WorkerLostError after a couple of requests.
# fig.remove()
# fig.parent.close_scene(fig)
# this doesn't work on centos:
# mlab.close()
with open('fig.png', 'rb') as f:
buf = f.read()
return buf
def show(self): '''Show the 3D diagram in the screen.''' from mayavi import mlab self.triangleMesh= mlab.triangular_mesh(self.x, self.y, self.z, self.triangles, scalars= self.scalars) mlab.colorbar(self.triangleMesh, orientation='vertical') mlab.outline(self.triangleMesh) mlab.axes(self.triangleMesh, xlabel= self.axialForceLabel, ylabel= self.bendingMomentYLabel, zlabel= self.bendingMomentZLabel) #mlab.title(self.title) mlab.show()
def draw_mesh(self, mesh, color=WHITE, opacity=0.7):
x, y, z, triangles = self._get_triangular_mesh(mesh)
mlab.triangular_mesh(x, y, z, triangles, color=color,
opacity=opacity, representation='surface')
#mlab.triangular_mesh(x, y, z, triangles, colormap='bone',
# opacity=0.8, representation='surface')
mlab.triangular_mesh(x, y, z, triangles, color=(0, 0, 0),
line_width=1.0, representation='wireframe')
mlab.outline()
mlab.axes()
def _add_points(self, scene, name=None, new=None):
scene.disable_render = True
mlab.clf(figure=scene)
x,y,z = np.random.rand(3,50)
mlab.points3d(x,y,z, figure=scene.mayavi_scene )
mlab.axes()
scene.disable_render = False
def labels(self):
'''
Add 3d text to show the axes.
'''
fontsize = max(self.xrang, self.yrang)/40.
tcolor = (1,1,1)
mlab.text3d(self.xrang/2,-10,self.zrang+10,'R.A.',scale=fontsize,orient_to_camera=True,color=tcolor)
mlab.text3d(-10,self.yrang/2,self.zrang+10,'Decl.',scale=fontsize,orient_to_camera=True,color=tcolor)
mlab.text3d(-10,-10,self.zrang/2-10,'V (km/s)',scale=fontsize,orient_to_camera=True,color=tcolor)
# Add scale bars
if self.leng != 0.0:
distance = self.dist * 1e3
length = self.leng
leng_pix = np.round(length/distance/np.pi*180./np.abs(self.hdr['cdelt1']))
bar_x = [self.xrang-20-leng_pix, self.xrang-20]
bar_y = [self.yrang-10, self.yrang-10]
bar_z = [0, 0]
mlab.plot3d(bar_x, bar_y, bar_z, color=tcolor, tube_radius=1.)
mlab.text3d(self.xrang-30-leng_pix,self.yrang-25,0,'{:.2f} pc'.format(length),scale=fontsize,orient_to_camera=False,color=tcolor)
if self.vsp != 0.0:
vspan = self.vsp
vspan_pix = np.round(vspan/np.abs(self.hdr['cdelt3']/1e3))
bar_x = [self.xrang, self.xrang]
bar_y = [self.yrang-10, self.yrang-10]
bar_z = np.array([5, 5+vspan_pix])*self.zscale
mlab.plot3d(bar_x, bar_y, bar_z, color=tcolor, tube_radius=1.)
mlab.text3d(self.xrang,self.yrang-25,10,'{:.1f} km/s'.format(vspan),scale=fontsize,orient_to_camera=False,color=tcolor,orientation=(0,90,0))
# Label the coordinates of the corners
# Lower left corner
ra0 = self.extent[0]; dec0 = self.extent[2]
c = SkyCoord(ra=ra0*u.degree, dec=dec0*u.degree, frame='icrs')
RA_ll = str(int(c.ra.hms.h))+'h'+str(int(c.ra.hms.m))+'m'+str(round(c.ra.hms.s,1))+'s'
mlab.text3d(0,-10,self.zrang+5,RA_ll,scale=fontsize,orient_to_camera=True,color=tcolor)
DEC_ll = str(int(c.dec.dms.d))+'d'+str(int(abs(c.dec.dms.m)))+'m'+str(round(abs(c.dec.dms.s),1))+'s'
mlab.text3d(-40,0,self.zrang+5,DEC_ll,scale=fontsize,orient_to_camera=True,color=tcolor)
# Upper right corner
ra0 = self.extent[1]; dec0 = self.extent[3]
c = SkyCoord(ra=ra0*u.degree, dec=dec0*u.degree, frame='icrs')
RA_ll = str(int(c.ra.hms.h))+'h'+str(int(c.ra.hms.m))+'m'+str(round(c.ra.hms.s,1))+'s'
mlab.text3d(self.xrang,-10,self.zrang+5,RA_ll,scale=fontsize,orient_to_camera=True,color=tcolor)
DEC_ll = str(int(c.dec.dms.d))+'d'+str(int(abs(c.dec.dms.m)))+'m'+str(round(abs(c.dec.dms.s),1))+'s'
mlab.text3d(-40,self.yrang,self.zrang+5,DEC_ll,scale=fontsize,orient_to_camera=True,color=tcolor)
# V axis
if self.extent[5] > self.extent[4]:
v0 = self.extent[4]; v1 = self.extent[5]
else:
v0 = self.extent[5]; v1 = self.extent[4]
mlab.text3d(-10,-10,self.zrang,str(round(v0,1)),scale=fontsize,orient_to_camera=True,color=tcolor)
mlab.text3d(-10,-10,0,str(round(v1,1)),scale=fontsize,orient_to_camera=True,color=tcolor)
mlab.axes(self.field, ranges=self.extent, x_axis_visibility=False, y_axis_visibility=False, z_axis_visibility=False)
mlab.outline()
def show_surface(pth):
"""
show surface from a h5
"""
mlab.figure()
cap = h5py.File(pth)
v = numpy.array(cap['vertices'])
t = numpy.array(cap['triangles'])
mlab.triangular_mesh(v[:,0], v[:,1], v[:,2], t)
mlab.axes()
def scatter3d(results,
outcomes,
policy=None):
'''
Function for making a 3d scatter plots. This function will plot
the 3 supplied outcomes against each other over time. If the data
is a time series, end states will be used.
:param results: The return from :meth:`perform_experiments`.
:param outcomes: The names of the 3 outcomes of interest that are to be
plotted.
:param policy: Optional argument, if provided, only for that particular
policy the scatter plot is generated. It is *recommended*
that this argument is provided if there are indeed multiple
policies.
'''
if len(outcomes)!=3:
raise EMAError("you provided %s outcomes, while you should supply 3" % (len(outcomes)))
#prepare the data
experiments, results = results
#get the results for the specific outcome of interest
results1 = results.get(outcomes[0])
results2 = results.get(outcomes[1])
results3 = results.get(outcomes[2])
results = [results1, results2, results3]
#restrict to policy if provided
if policy:
logical = experiments['policy'] == policy
results = [entry[logical] for entry in results]
#convert time series
temp = []
for entry in results:
if len(entry.shape) > 1:
if (entry.shape[1]>1):
entry = entry[:,-1]
temp.append(entry)
results = temp
#visualize results
mlab.figure(1, bgcolor=(1, 1, 1), fgcolor=(0, 0, 0))
extent = [0,1,0,1,0,1]
s = mlab.points3d(results[0],results[1], results[2],
extent=extent, mode='point')
mlab.axes(xlabel=outcomes[0],
ylabel=outcomes[1],
zlabel = outcomes[2],
)
mlab.show()
def plot_kern_3d(kern):
"""
Plot a ndarray -> do not use with big arrays !! it costs a lot
:param kern:
:return: plot the graph
"""
# noinspection PyUnusedLocal
figure = mlab.figure('DensityPlot')
mlab.points3d(kern)
mlab.axes()
mlab.show()
def axe(labs, rgs, f):
"""
add an axes object to the plot
labs - list of axis labels
rgs - array of axis ranges, may be produced by rgs
f - figure to which to add the axes
"""
try:
ml.axes(xlabel=labs[0],
ylabel=labs[1],
zlabel=labs[2],
ranges=rgs,
extent=ex,
nb_labels=5,
figure=f)
except:
ml.axes(xlabel=labs[0],
ylabel=labs[1],
zlabel=labs[2],
ranges=rgs,
extent=ex,
figure=f)
def visualize(self, max_dist=0.1):
try:
from mayavi import mlab
except:
print("mayavi is not installed!")
figure = mlab.figure('Signed Density Field')
SCALE = 100 # The dimensions will be expressed in cm for better visualization.
data = np.copy(self.data)
data = np.minimum(max_dist, data)
xmin, ymin, zmin = SCALE * self.origin
xmax, ymax, zmax = SCALE * self.max_coords
delta = SCALE * self.delta
xi, yi, zi = np.mgrid[xmin:xmax:delta, ymin:ymax:delta,
zmin:zmax:delta]
data[data <= 0] -= 0.2
data = -data
grid = mlab.pipeline.scalar_field(xi, yi, zi, data)
vmin = np.min(data)
vmax = np.max(data)
mlab.pipeline.volume(grid, vmin=vmin, vmax=(vmax + vmin) / 2)
mlab.axes()
mlab.show()
def plot_cone_surface(X, Y, Z):
# Some parameters (note size only really changes scale on axis)
#sizeX,sizeY = 1,2
#amplitude = 1
#nPoints = 500
# Calculate wavenumbers
#kx = nX*pi/sizeX
#ky = nY*pi/sizeY
x = np.array(X)
y = np.array(Y)
z = np.array(Z) #amplitude*np.sin(kx*X)*np.sin(ky*Y)
xyz = np.vstack([x, y, z])
kde = stats.gaussian_kde(xyz)
density = kde(xyz)
# Plot scatter with mayavi
figure = mlab.figure('DensityPlot')
pts = mlab.points3d(x, y, z, density, scale_mode='none', scale_factor=0.07)
mlab.axes()
mlab.show()
'''fig = plt.figure()
def make_frame(t):
mlab.clf()
src = mlab.pipeline.scalar_field(b)
m = mlab.pipeline.iso_surface(src,
contours=[0.8, 0.9, 1],
opacity=0.3,
colormap='Blues',
figure=fig_myv)
mlab.axes(ranges=[-650, 650, -650, 650, -350, 350],
color=(0, 0, 0),
nb_labels=5,
xlabel='X(pc)',
ylabel='Y(pc)',
zlabel='Z(pc)',
figure=fig_myv)
mlab.view(azimuth=0, elevation=0, distance=500, figure=fig_myv)
#m.scene.camera.elevation(-95)
m.scene.camera.elevation(-10 * t)
m.scene.camera.orthogonalize_view_up()
#m.scene.camera.compute_view_plane_normal()
return mlab.screenshot(antialiased=True)
def plot(self,lim=None):
from mayavi import mlab
if lim is None:
# Calculate limits
mus = np.concatenate(tuple([[N.mean] for N in filter(lambda N: N is not None, self.numN+self.denN)]), axis=0)
maxs = np.amax(mus,axis=0) + 1
mins = np.amin(mus,axis=0) - 1
s = np.amax(maxs-mins) / 2
mid = (maxs + mins) / 2
lim = [[mid[i]-1.2*s, mid[i]+1.2*s] for i in range(maxs.shape[0])]
if len(lim) == 3:
# Evaluate
xi,yi,zi = np.mgrid[lim[0][0]:lim[0][1]:50j, lim[1][0]:lim[1][1]:50j, lim[2][0]:lim[2][1]:50j]
coords = np.vstack([item.ravel() for item in [xi, yi, zi]])
density = self.evaluate(coords.T).reshape(xi.shape)
# Plot scatter with mayavi
figure = mlab.figure('DensityPlot')
grid = mlab.pipeline.scalar_field(xi, yi, zi, density)
minval = 0
maxval = density.max()
mlab.pipeline.volume(grid, vmin=minval, vmax=minval + .5*(maxval-minval))
mlab.axes()
mlab.show()
def surface_3d():
"""
使用Mayavi将二维数组绘制成3D曲面 x * exp(x**2 - y**2)
:return:
"""
import numpy as np
# create data
x, y = np.ogrid[-2:2:20j, -2:2:20j]
z = x * np.exp(-x**2 - y**2)
# view it
from mayavi import mlab
# 绘制一个三维空间中的曲面
pl = mlab.surf(x, y, z, warp_scale="auto")
# 在三维空间中添加坐标轴
mlab.axes(xlabel='x', ylabel='y', zlabel='z')
# 在三维空间中添加曲面区域的外框
mlab.outline(pl)
mlab.show()
def test_baxter_gripper():
mesh_filename = '/home/jmahler/jeff_working/GPIS/data/grippers/baxter/gripper.obj'
of = objf.ObjFile(mesh_filename)
gripper_mesh = of.read()
gripper_mesh.center_vertices_bb()
#gripper_mesh.rescale(0.9) # to make fingertips at the wide 0.67 distance
oof = objf.ObjFile(mesh_filename)
oof.write(gripper_mesh)
T_mesh_world = stf.SimilarityTransform3D(pose=tfx.pose(np.eye(4)), from_frame='world', to_frame='mesh')
R_grasp_gripper = np.array([[0, 0, -1],
[0, 1, 0],
[1, 0, 0]])
R_mesh_gripper = np.array([[1, 0, 0],
[0, 1, 0],
[0, 0, 1]])
t_mesh_gripper = np.array([0.005, 0.0, 0.055])
T_mesh_gripper = stf.SimilarityTransform3D(pose=tfx.pose(R_mesh_gripper, t_mesh_gripper),
from_frame='gripper', to_frame='mesh')
T_gripper_world = T_mesh_gripper.inverse().dot(T_mesh_world)
T_grasp_gripper = stf.SimilarityTransform3D(pose=tfx.pose(R_grasp_gripper), from_frame='gripper', to_frame='grasp')
T_mesh_gripper.save('/home/jmahler/jeff_working/GPIS/data/grippers/baxter/T_mesh_gripper.stf')
T_grasp_gripper.save('/home/jmahler/jeff_working/GPIS/data/grippers/baxter/T_grasp_gripper.stf')
gripper_params = {}
gripper_params['min_width'] = 0.026
gripper_params['max_width'] = 0.060
f = open('/home/jmahler/jeff_working/GPIS/data/grippers/baxter/params.json', 'w')
json.dump(gripper_params, f)
MayaviVisualizer.plot_pose(T_mesh_world, alpha=0.05, tube_radius=0.0025, center_scale=0.005)
MayaviVisualizer.plot_pose(T_gripper_world, alpha=0.05, tube_radius=0.0025, center_scale=0.005)
MayaviVisualizer.plot_mesh(gripper_mesh, T_mesh_world, style='surface', color=(1,1,1))
mv.axes()
def animateGIF(filename, prices):
'''Creates a mayavi visualization of a pd DataFrame containing stock prices
Then uses MoviePy to animate and save as a gif
Inputs:
prices => a pd DataFrame, w/ index: dates; columns: company names
'''
#Imports mlab here to delay starting of mayavi engine until necessary
from mayavi import mlab
#Because of current mayavi requirements, replaces dates and company names with integers
x_length, y_length = prices.shape
xTime = np.array([
list(xrange(x_length)),
] * y_length).transpose()
yCompanies = np.array([
list(xrange(y_length)),
] * x_length)
#Sort indexed prices by total return on last date
lastDatePrices = prices.iloc[-1]
lastDatePrices.sort_values(inplace=True)
sortOrder = lastDatePrices.index
zPrices = prices[sortOrder]
#Create mayavi2 object
fig = mlab.figure(bgcolor=(.4, .4, .4))
vis = mlab.surf(xTime, yCompanies, zPrices)
mlab.outline(vis)
mlab.orientation_axes(vis)
mlab.axes(vis,
nb_labels=0,
xlabel='Time',
ylabel='Company',
zlabel='Price')
animation = mpy.VideoClip(make_frame, duration=4).resize(1.0)
animation.write_gif(filename, fps=20)
def visualize_data(ast, Ug_array, grid):
nx = grid['nx']
ny = grid['ny']
nz = grid['nz']
xg = grid['xg']
yg = grid['yg']
zg = grid['zg']
# plot some contour plots in mayavi
# engine = mayavi.api.Engine()
# engine.start()
# scene = engine.scenes[0]
potential_fig = mlab.figure(figure=None)
mesh = wavefront.draw_polyhedron_mayavi(ast.V, ast.F, potential_fig)
# contour plot
# contour3d = mlab.contour3d(xg, yg, zg, Ug_array, figure=potential_fig)
# volume rendering
# volume = mlab.pipeline.volume(mlab.pipeline.scalar_field(Ug_array))
f = mlab.pipeline.scalar_field(xg, yg, zg, Ug_array)
v = mlab.pipeline.volume(f, vmin=0, vmax=0.2)
# cut planes
mlab.pipeline.image_plane_widget(f,
plane_orientation='x_axes',
slice_index=nx / 2)
mlab.pipeline.image_plane_widget(f,
plane_orientation='y_axes',
slice_index=ny / 2)
mlab.pipeline.image_plane_widget(f,
plane_orientation='z_axes',
slice_index=nz / 2)
mlab.outline()
mlab.axes()
mlab.colorbar(object=mesh, title='mm/sec^2')
def visualizePrices(prices):
'''Creates a mayavi visualization of a pd DataFrame containing stock prices
Inputs:
prices => a pd DataFrame, w/ index: dates; columns: company names
'''
#Imports mlab here to delay starting of mayavi engine until necessary
from mayavi import mlab
#Because of current mayavi requirements, replaces dates and company names with integers
x_length, y_length = prices.shape
xTime = np.array([
list(xrange(x_length)),
] * y_length).transpose()
yCompanies = np.array([
list(xrange(y_length)),
] * x_length)
#Sort indexed prices by total return on last date
lastDatePrices = prices.iloc[-1]
lastDatePrices.sort_values(inplace=True)
sortOrder = lastDatePrices.index
zPrices = prices[sortOrder]
#Create mayavi2 object
fig = mlab.figure(bgcolor=(.4, .4, .4))
vis = mlab.surf(xTime, yCompanies, zPrices)
mlab.outline(vis)
mlab.orientation_axes(vis)
#mlab.title('S&P 500 Market Data Visualization', size = .25)
mlab.axes(vis,
nb_labels=0,
xlabel='Time',
ylabel='Company',
zlabel='Price')
mlab.show()
def visualize(tetrahedrons,
save=False,
file_name='tetrahedron_mesh.vtu',
just_surface=True,
octmps_output_file='ClassI_ScattFilt.out'):
if just_surface:
data = get_surface_structure(tetrahedrons)
else:
data = get_complete_structure(tetrahedrons)
# Saving as VTU file
if save:
write_data(data, file_name=file_name)
mlab.figure(figure='OCTMPS', fgcolor=(1, 1, 1), bgcolor=(0.5, 0.5, 0.5))
src = VTKDataSource(data=data)
surf = mlab.pipeline.surface(src, opacity=0.01)
mlab.axes()
mlab.pipeline.surface(mlab.pipeline.extract_edges(surf),
color=(1, 1, 1),
line_width=0.0)
if octmps_output_file:
# Make the data and add it to the pipeline.
data, x_positions, z_positions = make_data(
octmps_output_file=octmps_output_file)
data = np.array([data]).swapaxes(1, 0)
src = ArraySource(transpose_input_array=True)
src.scalar_data = data
src.spacing = (x_positions[1] - x_positions[0], 0.,
z_positions[1] - z_positions[0])
src.origin = (x_positions[0], 0.0, z_positions[0])
mlab.pipeline.surface(src, colormap='jet')
mlab.colorbar(orientation='vertical', title='Reflectance')
mlab.show()
def m_field_wire(ori, pos, grid, x_grid, y_grid, z_grid, x_field, y_field,
z_field, no_lines):
fig = mplt.figure()
X, Y, Z = np.meshgrid(x_grid, y_grid, z_grid, indexing='ij')
for orientation, location in zip(ori, pos):
# draw sphere for point charge
wire(orientation, location, grid)
# draw electric field lines
line = mplt.flow(X,
Y,
Z,
x_field,
y_field,
z_field,
figure=fig,
seedtype='line',
integration_direction='both')
# number of integration steps
line.stream_tracer.maximum_propagation = 200
mplt.axes()
# set view to x-axis coming out of screen
fig.scene.x_plus_view()
mplt.draw(figure=fig)
mplt.show()
def main():
mu = np.array([1, 10, 20])
sigma = np.matrix([[20, 10, 10],
[10, 25, 1],
[10, 1, 50]])
np.random.seed(100)
data = np.random.multivariate_normal(mu, sigma, 1000)
values = data.T
kde = stats.gaussian_kde(values)
# Create a regular 3D grid with 50 points in each dimension
xmin, ymin, zmin = data.min(axis=0)
xmax, ymax, zmax = data.max(axis=0)
xi, yi, zi = np.mgrid[xmin:xmax:50j, ymin:ymax:50j, zmin:zmax:50j]
# Evaluate the KDE on a regular grid...
coords = np.vstack([item.ravel() for item in [xi, yi, zi]])
density = kde(coords).reshape(xi.shape)
# Visualize the density estimate as isosurfaces
mlab.contour3d(xi, yi, zi, density, opacity=0.5)
mlab.axes()
mlab.show()
def axes(plot,
nlabels=5,
extent=None,
ranges=None,
color=(0, 0, 0),
width=2,
fmt="%-#.2f"):
"""
Add an Axes module to a Mayavi2 plot or dataset.
Parameters:
* plot
Either the plot (as returned by one of the plotting functions of this
module) or a TVTK dataset.
* nlabels : int
Number of labels on the axes
* extent : list = [xmin, xmax, ymin, ymax, zmin, zmax]
Default if the objects extent.
* ranges : list = [xmin, xmax, ymin, ymax, zmin, zmax]
What will be display in the axes labels. Default is *extent*
* color : tuple = (r, g, b)
RGB of the color of the axes and text
* width : float
Line width
* fmt : str
Label number format
Returns:
* axes : Mayavi axes instace
The axes object in the pipeline
"""
_lazy_import_mlab()
a = mlab.axes(plot, nb_labels=nlabels, color=color)
a.label_text_property.color = color
a.title_text_property.color = color
if extent is not None:
a.axes.bounds = extent
if ranges is not None:
a.axes.ranges = ranges
a.axes.use_ranges = True
a.property.line_width = width
a.axes.label_format = fmt
a.axes.x_label, a.axes.y_label, a.axes.z_label = "N", "E", "Z"
return a
def scene_style(objs: dict, **kwargs) -> None:
sc = mlab.scalarbar(
objs["streamlines"],
title="Field\nStrength [T]",
orientation="vertical",
nb_labels=4,
)
# horizontal and vertical position from left->right, bottom->top
sc.scalar_bar_representation.position = np.array([0.85, 0.1])
# width and height of colourbar
sc.scalar_bar_representation.position2 = np.array([0.1, 0.8])
# The title of colourbar does not scale so we need to manually set it
sc.scalar_bar.unconstrained_font_size = True
sc.title_text_property.font_size = 20
sc.label_text_property.font_size = 20
ax = mlab.axes()
mlab.view(azimuth=42, elevation=73)
def axes(scene, show_axis_labels, view):
axes = mlab.axes(scene, nb_labels=1, line_width=3)
axes.axes.label_format = ''
if show_axis_labels == True:
axes.axes.x_label = 'x'
if view == 'front-parallel':
axes.axes.y_label = 'z'
axes.axes.z_label = ''
elif view == 'top-parallel':
axes.axes.y_label = ''
axes.axes.z_label = 'y'
else:
axes.axes.y_label = 'z'
axes.axes.z_label = 'y'
else:
axes.axes.x_label = ''
axes.axes.y_label = ''
axes.axes.z_label = ''
def animate_3d_mrt_observations(dataset, embedding, observations):
"""Animate Observation with sensor vector embedding in 3D space using mayavi
Args:
dataset (:obj:`CASASDataset`): CASAS dataset class containing
sensor information.
embedding (:obj:`numpy.ndarray`): A 2D array of size
(#sensors, #vec_ndim) containing vector embedding of each sensor.
observations (:obj:`list`): List of observations. Each observation is
a :obj:`list` of index or target name of sensors that are ON,
PRESENT or OPEN (depends on what type of sensor it is) at each
time step.
"""
figure = mlab.figure(dataset.data_dict['name'])
figure.scene.disable_render = True
points = mlab.points3d(embedding[:, 0], embedding[:, 1], embedding[:, 2],
scale_factor=0.03)
for i, x in enumerate(embedding):
mlab.text3d(x[0], x[1], x[2], dataset.sensor_list[i]['name'],
scale=(0.02, 0.02, 0.02))
points.glyph.scale_mode = 'scale_by_vector'
points.mlab_source.dataset.point_data.vectors = np.tile(
np.ones(embedding.shape[0]), (3, 1))
color_vector = np.zeros(embedding.shape[0])
points.mlab_source.dataset.point_data.scalars = color_vector
mlab.outline(None, color=(.7, .7, .7), extent=[-1, 1, -1, 1, -1, 1])
ax = mlab.axes(None, color=(.7, .7, .7), extent=[-1, 1, -1, 1, -1, 1],
ranges=[-1, 1, -1, 1, -1, 1], nb_labels=6)
ax.label_text_property.font_size = 3
ax.axes.font_factor = 0.4
figure.scene.disable_render = False
@mlab.animate(delay=250)
def anim():
f = mlab.gcf()
while True:
for observation in observations:
color_vector[:] = 0
color_vector[observation] = 1
points.mlab_source.dataset.point_data.scalars = color_vector
yield
anim()
mlab.show()
def plot_3d(img, slice=False, axis='z', color=None, size=(1000, 800)):
"""Visualize 3D segmentation results via mayavi"""
res = None
try:
img = img.astype(np.uint16)
assert img.ndim == 3, "Invalid dimension of 3D image: {}".format(
img.ndim)
bg_color = colors.to_rgb("black")
depth, height, width = img.shape
mlab.figure(bgcolor=bg_color, size=size)
axes_extent = [0, height, 0, width, 0, depth]
xlabel, ylabel, zlabel = 'X', 'Y', 'Z'
if slice:
if axis == 'z':
res = mlab.volume_slice(img, colormap='Vega20')
axes_extent = [0, depth, 0, height, 0, width]
xlabel, zlabel = 'Z', 'X'
else:
res = mlab.volume_slice(img.transpose((1, 2, 0)),
colormap='Vega20')
else:
if color is not None:
res = mlab.contour3d(img.transpose((1, 2, 0)), color=color)
else:
res = mlab.contour3d(img.transpose((1, 2, 0)),
contours=10,
transparent=True)
# axes feature configuration
ax = mlab.axes(line_width=0.5,
extent=axes_extent,
xlabel=xlabel,
ylabel=ylabel,
zlabel=zlabel)
ax.axes.font_factor = 0.75
mlab.outline()
except FileNotFoundError:
print("3D segmentation array loading unsuccessful")
return res
def plot_3d_sensor_vector(dataset, embedding):
"""Plot sensor embedding in 3D space using mayavi
Args:
"""
figure = mlab.figure('Sensor Embedding (3D)')
figure.scene.disable_render = True
points = mlab.points3d(embedding[:, 0], embedding[:, 1], embedding[:, 2],
scale_factor=0.03)
for i, x in enumerate(embedding):
mlab.text3d(x[0], x[1], x[2], dataset.sensor_list[i]['name'],
scale=(0.02, 0.02, 0.02))
mlab.outline(None, color=(.7, .7, .7), extent=[-1, 1, -1, 1, -1, 1])
ax = mlab.axes(None, color=(.7, .7, .7), extent=[-1, 1, -1, 1, -1, 1],
ranges=[-1, 1, -1, 1, -1, 1], nb_labels=6)
ax.label_text_property.font_size = 3
ax.axes.font_factor = 0.4
figure.scene.disable_render = False
mlab.show()
def disp_3d_contour(self, size=(1000, 800)):
depth, height, width = self.masks.shape
bg_color = colors.to_rgb("black")
axes_extent = [0, height, 0, width, 0, depth]
xlabel, ylabel, zlabel = 'X', 'Y', 'Z'
mlab.figure(bgcolor=bg_color, size=size)
res = mlab.contour3d(self.masks.transpose((1, 2, 0)),
contours=10,
transparent=True)
ax = mlab.axes(line_width=0.5,
extent=axes_extent,
xlabel=xlabel,
ylabel=ylabel,
zlabel=zlabel)
ax.axes.font_factor = 0.75
mlab.outline()
return res
def redraw_scene(self, scene, cur_scatter_data):
# Notice how each mlab call points explicitely to the figure it
# applies to.
mlab.clf(figure=scene.mayavi_scene)
x = cur_scatter_data[0]
y = cur_scatter_data[1]
z = cur_scatter_data[2]
xlabel_text = cur_scatter_data[3][0]
ylabel_text = cur_scatter_data[3][1]
zlabel_text = cur_scatter_data[3][2]
cur_colors = cur_scatter_data[4]
cur_scales = [np.array(x) for x in cur_scatter_data[5]]
label_unique = cur_scatter_data[6]
points_dict.clear()
for ii in range(len(label_unique)):
points_dict[label_unique[ii]] = mlab.points3d(
x[ii],
y[ii],
z[ii],
cur_scales[ii] * self.cur_scale,
color=cur_colors[ii][0],
scale_factor=0.01,
opacity=self.cur_opacity / 100)
for ii in range(len(outputs_unique)):
mlab.text(0.02,
1 - 0.035 * (ii + 1),
'-' + str(outputs_unique[ii]),
width=0.06,
color=all_colors[ii])
cur_axex = mlab.axes(xlabel=xlabel_text,
ylabel=ylabel_text,
zlabel=zlabel_text,
extent=[
min(sum(x, [])),
max(sum(x, [])),
min(sum(y, [])),
max(sum(y, [])),
min(sum(z, [])),
max(sum(z, []))
])
cur_axex.axes.font_factor = 0.8
def plot3d_embeddings(dataset, embeddings, figure=None):
"""Plot sensor embedding in 3D space using mayavi.
Given the dataset and a sensor embedding matrix, each sensor is shown as
a sphere in the 3D space. Note that the shape of embedding matrix is
(num_sensors, 3) where num_sensors corresponds to the length of
``dataset.sensor_list``. All embedding vectors range between 0 and 1.
Args:
dataset (:obj:`~pymrt.casas.CASASDataset`): CASAS smart home dataset.
embeddings (:obj:`numpy.ndarray`): 3D sensor vector embedding.
"""
show_figure = False
if figure is None:
show_figure = True
figure = mlab.figure('Sensor Embedding (3D)')
# Plot sensors, texts and outlines
figure.scene.disable_render = True
points = mlab.points3d(embeddings[:, 0],
embeddings[:, 1],
embeddings[:, 2],
scale_factor=0.015)
for i, x in enumerate(embeddings):
mlab.text3d(x[0],
x[1],
x[2],
dataset.sensor_list[i]['name'],
scale=(0.01, 0.01, 0.01))
mlab.outline(None, color=(.7, .7, .7), extent=[0, 1, 0, 1, 0, 1])
ax = mlab.axes(None,
color=(.7, .7, .7),
extent=[0, 1, 0, 1, 0, 1],
ranges=[0, 1, 0, 1, 0, 1],
nb_labels=6)
ax.label_text_property.font_size = 3
ax.axes.font_factor = 0.3
figure.scene.disable_render = False
if show_figure:
mlab.show()
return figure, points
def show_mayavi(x, y, z, res):
fig = mlab.figure(bgcolor=(1, 1, 1), size=(640, 480))
mlab.outline(color=(0, 0, 0))
res = np.asarray(res)
xx, yy = np.mgrid[-10:10:0.5, -10:10:0.5]
zz = res[0] * xx + res[1] * yy + res[2]
# z /= 4
# mlab.surf(xx, yy, zz, color=(0, 0, 1), warp_scale=.25, representation='wireframe', line_width=0.5)
# mlab.points3d(x, y, z, color=(1, 0, 0), scale_factor=.3, figure=fig)
mlab.points3d(x, y, z, color=(1, 0, 0), mode='point', figure=fig)
axes = mlab.axes(color=(0, 0, 0), nb_labels=5)
axes.title_text_property.color = (0.0, 0.0, 0.0)
axes.title_text_property.font_family = 'times'
axes.label_text_property.color = (0.0, 0.0, 0.0)
axes.label_text_property.font_family = 'times'
mlab.gcf().scene.parallel_projection = True
mlab.orientation_axes()
mlab.show()
def disp_3d_slice(self, axis='z'):
"""Display 3D segmentation results interactively along z-axis or y-axis"""
depth, height, width = self.masks.shape
bg_color = colors.to_rgb("black")
axes_extent = [0, depth, 0, height, 0, width]
xlabel, ylabel, zlabel = 'X', 'Y', 'Z'
if axis == 'z':
res = mlab.volume_slice(self.masks, colormap='Vega20')
axes_extent = [0, depth, 0, height, 0, width]
xlabel, zlabel = 'Z', 'X'
else:
res = mlab.volume_slice(self.masks.transpose((1, 2, 0)),
colormap='Vega20')
ax = mlab.axes(line_width=0.5,
extent=axes_extent,
xlabel=xlabel,
ylabel=ylabel,
zlabel=zlabel)
ax.axes.font_factor = 0.75
mlab.outline()
return res
def draw_ply(array_in, array_out):
mlab.figure(bgcolor=(1, 1, 1), size=(640, 480))
mlab.outline(color=(0, 0, 0))
mlab.points3d(array_in[:, 0],
array_in[:, 1],
array_in[:, 2],
color=(1, 0, 0),
mode='point')
mlab.points3d(array_out[:, 0],
array_out[:, 1],
array_out[:, 2],
color=(0, 0, 1),
mode='point')
axes = mlab.axes(color=(0, 0, 0), nb_labels=5)
axes.title_text_property.color = (0.0, 0.0, 0.0)
axes.title_text_property.font_family = 'times'
axes.label_text_property.color = (0.0, 0.0, 0.0)
axes.label_text_property.font_family = 'times'
mlab.gcf().scene.parallel_projection = True
mlab.orientation_axes()
mlab.show()
def vis_multiple(multi_points,
save_folder,
save_name,
normalize=True,
save_gif=True,
delete=False,
show=False):
# points = np.loadtxt(full_path, delimiter=',')
# points = points[:50, :]
fig = mlab.figure(size=(1024, 1024))
for idx, points in enumerate(multi_points):
if normalize:
points[:, :3] = pc_normalize(points[:, :3])
x, y, z = np.split(points[:, :3], 3, axis=-1)
# vx, vy, vz = np.split(points[:, 3:], 3, axis=-1)
if save_gif:
fig.scene.movie_maker.record = True
fig.scene.movie_maker.directory = './'
selected_color = colors[idx]
s = points3d(x,
y,
z,
color=selected_color,
scale_factor=0.01,
opacity=0.5)
# mlab.quiver3d(x, y, z, vx, vy, vz, mode='arrow', scale_factor=0.03)
# ms = s.mlab_source
# animate(ms, points, transformer)
axes = mlab.axes()
axes.axes.fly_mode = 'none'
axes.axes.bounds = np.array([0, 0.4, 0.4, 0., 0., 0.4])
mlab.title(save_name, size=0.1)
if show:
mlab.show()
if save_gif:
save(save_name=save_name, images_folder=save_folder, delete=delete)
#dataExport(4)
# In[2]:
n = 4
for i in range(n): #l=0,1,2,3
for j in range(-i, i + 1):
xdata = "xdata{}{}{}.dat".format(n, i, j)
ydata = "ydata{}{}{}.dat".format(n, i, j)
zdata = "zdata{}{}{}.dat".format(n, i, j)
magdata = "density{}{}{}.dat".format(n, i, j)
x = load(xdata)
y = load(ydata)
z = load(zdata)
density = load(magdata)
figure = mlab.figure('DensityPlot{}{}{}'.format(n, i, j))
mag = density / amax(density)
#pts = mlab.points3d(mag ,opacity =0.5, transparent=True)
pts = mlab.contour3d(mag, opacity=0.5)
mlab.colorbar(orientation='vertical')
mlab.axes()
mlab.savefig("{}{}{}_contour.png".format(n, i, j))
print "{}{}{}.png saved".format(n, i, j)
print "Completed"
# In[ ]:
#random_indices = random.sample(range(len(x)),5000)
#x = np.array([x[i] for i in sorted(random_indices)])
#y = np.array([y[i] for i in sorted(random_indices)])
#z = np.array([z[i] for i in sorted(random_indices)])
#vx = np.array([vx[i] for i in sorted(random_indices)])
#vy = np.array([vy[i] for i in sorted(random_indices)])
#vz = np.array([vz[i] for i in sorted(random_indices)])
xyz = np.vstack([x,y,z])
kde = stats.gaussian_kde(xyz, bw_method=0.1)
X, Y, Z = np.mgrid[x.min():x.max():100j, y.min():y.max():100j, z.min():z.max():100j]
positions = np.vstack([X.ravel(), Y.ravel(), Z.ravel()])
density = kde(positions).reshape(X.shape)
#Visualize the density estimate as isosurfaces
figure = mlab.figure('myfig')
figure.scene.disable_render = True # Super duper trick
mlab.contour3d(X, Y, Z, density, opacity=0.3, colormap = 'Blues', figure = figure)
#mlab.quiver3d(x, y, z, vx, vy, vz)
mlab.axes(extent = [-650, 650, -650, 650, -650, 650], ranges = [-650, 650, -650, 650, -650, 650], nb_labels = 7, figure = figure)
mlab.points3d(x_OB, y_OB, z_OB, np.full(len(x_OB),10), scale_factor=1, figure = figure)
OB_Names = ['gammavelorum', 'NGC2547', 'trumpler10', 'NGC2516', 'velaOB2', 'OriOB1', 'HIP22931', 'HIP27345', 'HIP33175', 'NGC2232', 'Bellatrix', 'Rigel', 'Alnilam', 'USco', 'UCL', 'LLC', 'IC2602', 'aCar', 'IC2391', 'HIP45189', 'NGC2451A', 'Col135', 'HIP28944']
for i in range(len(x_OB)):
mlab.text3d(x_OB[i], y_OB[i], z_OB[i], OB_Names[i], scale=5, figure = figure)
figure.scene.disable_render = False # Super duper trick
mlab.show()
delta = 0.025
a = 4.0
b = 10.0
sigma = 10.0
t, X = ms.int_translated_system(a=2.0, b=100, T=200000, x0=[0.8, 0.9, 0.5])
# t, X = ms.int_system( a = 4.0, b = 10.0, T = 400000, x0 = [0.9, 0.2, 0.5])
ux, vx, rhox = np.mgrid[0:1:50j, 0:1:50j, -0.5:0.5:50j]
# ux, vx, rhox = np.mgrid[0:1:50j, 0:1:50j, -1.0:1.0:50j]
# values = F(rhox + 0.5, ux, vx)
# mlab.contour3d(ux, vx, rhox, values, contours=[0], opacity = 0.3)
mlab.figure(size=(800, 600), bgcolor=(1, 1, 1), fgcolor=(0, 0, 0))
mlab.clf()
values = ms.G_t(rhox, ux, vx)
mlab.contour3d(ux, vx, rhox, values, contours=[0], opacity=0.5)
values = ms.fold_t(rhox, ux, vx)
mlab.contour3d(ux, vx, rhox, values, contours=[0], opacity=0.5)
mlab.plot3d(X[0, :],
X[1, :],
X[2, :],
color=(0, 0, 0),
line_width=2.0,
tube_radius=None)
mlab.points3d(X[0, 0], X[1, 0], X[2, 0], scale_factor=0.03, line_width=0.1)
mlab.axes(extent=[0, 1, 0, 1, -0.5, 0.5], xlabel='u', ylabel='v', zlabel='rho')
# mlab.axes(extent = [0, 1, 0, 1, -1.0, 1.0], xlabel = 'u', ylabel = 'v', zlabel = 'rho')
# mlab.outline(color = (0, 0, 0))
mlab.show()
def plot(self, x, y, z, mx, my, mz, scalars, fname, savefig=True):
'''
x,y,z,mx,my,mz为xyzdxdydz方式的数据
scalars:标量数据，可能用于标记颜色
fname:str,文件的名字
'''
figure = mlab.figure(bgcolor=self.bgcolor, size=self.size) #图片的
mlab.quiver3d(x,
y,
z,
mx,
my,
mz,
scalars=scalars,
colormap=self.colormap,
scale_mode=self.scale_mode,
scale_factor=self.scale_factor)
if self.show_colorbar:
mlab.colorbar(
title='Mz', #color 的名字
orientation='vertical', #垂直方向
nb_labels=5, #显示五个标签
label_fmt='%.1f') #保留一位小数
#坐标轴：
if self.show_axes:
#线宽，显示五个标签
mlab.axes(xlabel='x',
ylabel='y',
zlabel='z',
line_width=3.0,
nb_labels=5)
if self.show_outline:
#线宽2.0 ，有一点透明
mlab.outline(line_width=2.0, opacity=0.5)
for view in self.view:
mlab.view(view[0], view[1]) #观察角度
if isinstance(fname, str) and isinstance(self.save_path,
str) and savefig:
print('savefig in ', self.save_path)
if self.gpu:
mlab.savefig(os.path.join(
self.save_path, '%s-z%d-x%d.%s' %
(fname, view[0], view[1], self.fig_format)),
magnification=3)
else:
mlab.savefig(
os.path.join(
self.save_path, '%s-z%d-x%d.%s' %
(fname, view[0], view[1], self.fig_format)))
if self.show_fig:
print(
"Need to manually turn off the picture, will continue drawing!"
)
mlab.show() #显示图片
if not self.show_fig:
mlab.close(all=True) #关闭画布
