def __init__(self, *args, **kargs):
ArtGL.__init__(self, **kargs)
self.do_stencil_test = True
self._gl_offset = kargs.pop('gl_offset', (0, 0, 0.))
self._gl_3dpath = kargs.pop('gl_3dpath', None)
self._gl_facecolor = kargs.pop('gl_facecolor', None)
self._gl_edgecolor = kargs.pop('gl_edgecolor', None)
self._gl_solid_facecolor = kargs.pop('gl_solid_facecolor', None)
self._gl_solid_edgecolor = kargs.pop('gl_solid_edgecolor', None)
self._gl_shade = kargs.pop('gl_shade', 'smooth')
self._gl_lighting = kargs.pop('gl_lighting', True)
self._gl_facecolordata = kargs.pop('facecolordata', None)
self._gl_voffset = kargs.pop('view_offset', (0,0,0,0.))
self._gl_array_idx = kargs.pop('array_idx', None)
self._gl_use_pointfill = kargs.pop('use_pointfill', False)
self._cz = None
self._gl_cz = None
self._update_ec = True
self._update_fc = True
self._update_v = True
self._update_i = True
self._update_a = True
Poly3DCollection.__init__(self, *args, **kargs)
def update_scalarmappable(self):
if self._gl_solid_facecolor is not None:
f = cc.to_rgba(self._gl_solid_facecolor)
self._gl_facecolor = np.tile(f, (len(self._gl_3dpath[2]),1))
else:
if self._gl_cz:
if self._gl_facecolordata is not None:
self._gl_facecolor = self.to_rgba(self._gl_facecolordata)
elif self._gl_shade =='flat':
if self._gl_cz:
z = [np.mean(self._gl_3dpath[2][idx])
for idx in self._gl_3dpath[4]]
else:
z = [np.mean(self._gl_cz[idx])
for idx in self._gl_3dpath[4]]
z = np.array(z)
self._gl_facecolor = self.to_rgba(z)
else:
if self._gl_cz is None:
self._gl_facecolor = self.to_rgba(self._gl_3dpath[2])
else:
self._gl_facecolor = self.to_rgba(self._gl_cz)
if self._alpha is not None:
if self._gl_facecolor.ndim == 3:
self._gl_facecolor[:, :,-1]=self._alpha
else:
self._gl_facecolor[:,-1]=self._alpha
if self._gl_solid_edgecolor is not None:
f = cc.to_rgba(self._gl_solid_edgecolor)
self._gl_edgecolor = np.tile(f, (len(self._gl_3dpath[2]),1))
else:
if self._gl_shade == False:
z = [np.mean(self._gl_3dpath[2][idx])
for idx in self._gl_3dpath[4]]
z = np.array(z)
self._gl_edgecolor = self.to_rgba(z)
else:
self._gl_edgecolor = self.to_rgba(self._gl_3dpath[2])
if self._alpha is not None:
if self._gl_edgecolor.ndim == 3:
self._gl_edgecolor[:, :,-1]=self._alpha
else:
self._gl_edgecolor[:,-1]=self._alpha
Poly3DCollection.update_scalarmappable(self)
def polyplane(verts, alpha=0.1, color="green"):
poly = Poly3DCollection(verts)
poly.set_alpha(alpha)
poly.set_facecolor(color)
return poly
def animate(ii):
removePlt()
#ii=1
if ii<18:
dec = 90
inc = 0. + ii*5.
elif ii < 36:
dec = 270.
inc = 90. - (ii-18)*5.
elif ii < 54:
dec = 270.
inc = 0.+ (ii-36)*5.
else:
dec = 90
inc = 90. - (ii-54)*5.
ax1.axis('equal')
block_xyz = np.asarray([[-.2, -.2, .2, .2, 0],
[-.25, -.25, -.25, -.25, 0.5],
[-.2, .2, .2, -.2, 0]])*10.
block_xyz[1][:] -=20.
# rot = Utils.mkvc(Utils.dipazm_2_xyz(pinc, pdec))
# xyz = Utils.rotatePointsFromNormals(block_xyz.T, np.r_[0., 1., 0.], rot,
# np.r_[p.xc, p.yc, p.zc])
R = Utils.rotationMatrix(inc, dec)
xyz = R.dot(block_xyz).T
xyz[:,2] -= depth + dz/2.
#print xyz
# Face 1
ax1.add_collection3d(Poly3DCollection([zip(xyz[:4, 0],
xyz[:4, 1],
xyz[:4, 2])], facecolors='b'))
ax1.add_collection3d(Poly3DCollection([zip(xyz[[1, 2, 4], 0],
xyz[[1, 2, 4], 1],
xyz[[1, 2, 4], 2])], facecolors='b'))
ax1.add_collection3d(Poly3DCollection([zip(xyz[[0, 1, 4], 0],
xyz[[0, 1, 4], 1],
xyz[[0, 1, 4], 2])], facecolors='b'))
ax1.add_collection3d(Poly3DCollection([zip(xyz[[2, 3, 4], 0],
xyz[[2, 3, 4], 1],
xyz[[2, 3, 4], 2])], facecolors='b'))
ax1.add_collection3d(Poly3DCollection([zip(xyz[[0, 3, 4], 0],
xyz[[0, 3, 4], 1],
xyz[[0, 3, 4], 2])], facecolors='b'))
ax1.w_yaxis.set_ticklabels('')
ax1.w_yaxis.set_label_text('')
ax1.w_zaxis.set_ticklabels('')
ax1.w_zaxis.set_label_text('')
# block_xyz[1][:] +=20.
# # rot = Utils.mkvc(Utils.dipazm_2_xyz(pinc, pdec))
#
# # xyz = Utils.rotatePointsFromNormals(block_xyz.T, np.r_[0., 1., 0.], rot,
# # np.r_[p.xc, p.yc, p.zc])
#
# R = Utils.rotationMatrix(rinc, rdec)
#
# xyz = R.dot(block_xyz).T
# xyz[:,2] -= depth + dz/2.
#
# #print xyz
# # Face 1
# ax1.add_collection3d(Poly3DCollection([zip(xyz[:4, 0],
# xyz[:4, 1],
# xyz[:4, 2])], facecolors='y'))
#
# ax1.add_collection3d(Poly3DCollection([zip(xyz[[1, 2, 4], 0],
# xyz[[1, 2, 4], 1],
# xyz[[1, 2, 4], 2])], facecolors='y'))
#
# ax1.add_collection3d(Poly3DCollection([zip(xyz[[0, 1, 4], 0],
# xyz[[0, 1, 4], 1],
# xyz[[0, 1, 4], 2])], facecolors='y'))
#
# ax1.add_collection3d(Poly3DCollection([zip(xyz[[2, 3, 4], 0],
# xyz[[2, 3, 4], 1],
# xyz[[2, 3, 4], 2])], facecolors='y'))
#
# ax1.add_collection3d(Poly3DCollection([zip(xyz[[0, 3, 4], 0],
# xyz[[0, 3, 4], 1],
# xyz[[0, 3, 4], 2])], facecolors='y'))
MAG.plotObj3D(p, rx_h, View_elev, View_azim, npts2D, xylim, profile="X", fig= fig, axs = ax1, plotSurvey=False)
# Create problem
prob = PFlocal.problem()
prob.prism = p
prob.survey = srvy
prob.Bdec, prob.Binc, prob.Bigrf = dec, inc, Bigrf
prob.Q, prob.rinc, prob.rdec = Q, rinc, rdec
prob.uType, prob.mType = comp, 'total'
prob.susc = susc
# Compute fields from prism
b_ind, b_rem = prob.fields()
if irt == 'total':
out = b_ind + b_rem
elif irt == 'induced':
out = b_ind
else:
out = b_rem
#out = plogMagSurvey2D(prob, susc, Einc, Edec, Bigrf, x1, y1, x2, y2, comp, irt, Q, rinc, rdec, fig=fig, axs1=ax2, axs2=ax3)
#dat = axs1.contourf(X,Y, np.reshape(out, (X.shape)).T
global im1
im1 = ax1.contourf(X,Y,np.reshape(out, (X.shape)).T,20,zdir='z',offset=rx_h+5., clim=clim, vmin=clim[0],vmax=clim[1], cmap = 'RdBu_r')
ax5 = fig.add_axes([pos.x0 , pos.y0+0.25, pos.height*0.02, pos.height*0.4])
cb = plt.colorbar(im1,cax=ax5, orientation="vertical", ax = ax1, ticks=np.linspace(im1.vmin,im1.vmax, 4), format="${%.0f}$")
cb.set_label("$B^{TMI}\;(nT)$",size=12)
cb.ax.yaxis.set_ticks_position('left')
cb.ax.yaxis.set_label_position('left')
global im5
im5 = ax1.text(0,0,-60,'$B_0, I: ' + str(inc) + '^\circ, D: ' + str(dec) + '^\circ$', horizontalalignment='center')
H0 = (Bigrf,inc,dec)
actv = np.ones(mesh.nC)==1
# Create active map to go from reduce space to full
actvMap = Maps.InjectActiveCells(mesh, actv, -100)
nC = len(actv)
# Create a MAGsurvey
rxLoc = np.c_[Utils.mkvc(X), Utils.mkvc(Y), Utils.mkvc(Z)]
rxLoc = PF.BaseMag.RxObs(rxLoc)
srcField = PF.BaseMag.SrcField([rxLoc],param = H0)
survey = PF.BaseMag.LinearSurvey(srcField)
# We can now create a susceptibility model and generate data
# Lets start with a simple block in half-space
# model = np.zeros((mesh.nCx,mesh.nCy,mesh.nCz))
# model[(midx-2):(midx+2),(midy-2):(midy+2),-6:-2] = 0.02
# model = mkvc(model)
# model = model[actv]
# Create active map to go from reduce set to full
actvMap = Maps.InjectActiveCells(mesh, actv, -100)
# Creat reduced identity map
idenMap = Maps.IdentityMap(nP = nC)
# Create the forward model operator
probinv = PF.Magnetics.MagneticIntegral(mesh, mapping = idenMap, actInd = actv)
# Pair the survey and problem
survey.pair(probinv)
# Compute linear forward operator and compute some data
# d = probinv.fields(model)
# Plot the model
# m_true = actvMap * model
# m_true[m_true==-100] = np.nan
#plt.figure()
#ax = plt.subplot(212)
#mesh.plotSlice(m_true, ax = ax, normal = 'Y', ind=midy, grid=True, clim = (0., model.max()/3.), pcolorOpts={'cmap':'viridis'})
#plt.title('A simple block model.')
#plt.xlabel('x'); plt.ylabel('z')
#plt.gca().set_aspect('equal', adjustable='box')
# We can now generate data
data = out + np.random.randn(len(out)) # We add some random Gaussian noise (1nT)
wd = np.ones(len(data))*1. # Assign flat uncertainties
# Create distance weights from our linera forward operator
wr = np.sum(probinv.G**2.,axis=0)**0.5
wr = ( wr/np.max(wr) )
#survey.makeSyntheticData(data, std=0.01)
survey.dobs= data
survey.std = wd
survey.mtrue = model
# Create a regularization
reg = Regularization.Sparse(mesh, indActive=actv, mapping=idenMap)
reg.cell_weights = wr
dmis = DataMisfit.l2_DataMisfit(survey)
dmis.Wd = 1/wd
# Add directives to the inversion
opt = Optimization.ProjectedGNCG(maxIter=100 ,lower=0.,upper=1., maxIterLS = 20, maxIterCG= 10, tolCG = 1e-3)
invProb = InvProblem.BaseInvProblem(dmis, reg, opt)
betaest = Directives.BetaEstimate_ByEig()
# Here is where the norms are applied
# Use pick a treshold parameter empirically based on the distribution of model
# parameters (run last cell to see the histogram before and after IRLS)
IRLS = Directives.Update_IRLS( norms=([2,2,2,2]), eps=(2e-3,2e-3), f_min_change = 1e-3, minGNiter=3,beta_tol=1e-2)
update_Jacobi = Directives.Update_lin_PreCond()
inv = Inversion.BaseInversion(invProb, directiveList=[IRLS,betaest,update_Jacobi])
m0 = np.ones(nC)*1e-4
mrec = inv.run(m0)
# Here is the recovered susceptibility model
ypanel = midx
zpanel = -4
m_l2 = actvMap * reg.l2model
m_l2[m_l2==-100] = np.nan
m_lp = actvMap * mrec
m_lp[m_lp==-100] = np.nan
# m_true = actvMap * model
# m_true[m_true==-100] = np.nan
#Plot L2 model
#global im2
xx, zz = mesh.gridCC[:,0].reshape(mesh.vnC, order="F"), mesh.gridCC[:,2].reshape(mesh.vnC, order="F")
yy = mesh.gridCC[:,1].reshape(mesh.vnC, order="F")
temp = m_lp.reshape(mesh.vnC, order='F')
ptemp = temp[:,:,indz].T
#ptemp = ma.array(ptemp ,mask=np.isnan(ptemp))
global im2
im2 = ax2.contourf(xx[:,:,indz].T,yy[:,:,indz].T,ptemp,20, vmin = vmin, vmax= vmax, clim=[vmin,vmax])
ax2.plot(([mesh.vectorCCx[0],mesh.vectorCCx[-1]]),([mesh.vectorCCy[indy],mesh.vectorCCy[indy]]),color='w')
ax2.set_aspect('equal')
ax2.xaxis.set_visible(False)
ax2.set_xlim(-60,60)
ax2.set_ylim(-60,60)
ax2.set_title('Induced Model')
ax2.set_ylabel('Northing (m)',size=14)
ptemp = temp[:,indy,:].T
global im3
im3 = ax3.contourf(xx[:,indy,:].T,zz[:,indy,:].T,ptemp,20, vmin = vmin, vmax= vmax, clim=[vmin,vmax])
ax3.set_aspect('equal')
ax3.set_xlim(-60,60)
ax3.set_ylim(-60,0)
ax3.set_title('EW Section')
ax3.set_xlabel('Easting (m)',size=14)
ax3.set_ylabel('Elevation (m)',size=14)
ax4 = fig.add_axes([pos.x0 + 0.75, pos.y0+0.25, pos.height*0.02, pos.height*0.4])
cb = plt.colorbar(im3,cax=ax4, orientation="vertical", ax = ax1, ticks=np.linspace(im3.vmin,im3.vmax, 4), format="${%.3f}$")
cb.set_label("Susceptibility (SI)",size=12)
def show_fermi_surf(self, cell='bz', plot='mpl',
savefig='fs.png',
cmap='Spectral'):
'''
Plotting the Fermi surface within the BZ using matplotlib.
'''
try:
from skimage.measure import marching_cubes_lewiner as marching_cubes
except ImportError:
try:
from skimage.measure import marching_cubes
except ImportError:
raise ImportError("scikit-image not installed.\n"
"Please install with it with `conda install scikit-image` or `pip install scikit-image`")
bcell = self.atoms.get_reciprocal_cell()
b1, b2, b3 = np.linalg.norm(bcell, axis=1)
if cell == 'bz':
# the vertices, rigdges and facets of the BZ
p, l, f = get_brillouin_zone_3d(bcell)
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
# https://docs.scipy.org/doc/scipy/reference/tutorial/spatial.html#voronoi-diagrams
# cKDTree is implemented in cython, which is MUCH MUCH FASTER than KDTree
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
from scipy.spatial import cKDTree
px, py, pz = np.tensordot(
self.atoms.get_reciprocal_cell(),
np.mgrid[-1:2, -1:2, -1:2],
axes=[0, 0]
)
points = np.c_[px.ravel(), py.ravel(), pz.ravel()]
tree = cKDTree(points)
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
# Gamma point belong to the first BZ.
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
gamma_region_id = tree.query([0, 0, 0])[1]
else:
# the vertices, rigdges and facets of the primitive cell
p, l, f = get_primitive_cell_3d(bcell)
if plot.lower() == 'mpl':
############################################################
# Plot the Fermi surface using matplotlib
############################################################
import matplotlib as mpl
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
############################################################
fig = plt.figure(figsize=(6, 6))
ax = fig.add_subplot(111, projection='3d')
# ax.set_aspect('equal')
############################################################
basis_vector_clrs = ['r', 'g', 'b']
basis_vector_labs = ['x', 'y', 'z']
for ii in range(3):
ax.plot([0, bcell[ii, 0]], [0, bcell[ii, 1]], [0, bcell[ii, 2]],
color=basis_vector_clrs[ii], lw=1.5)
ax.text(bcell[ii, 0], bcell[ii, 1], bcell[ii, 2],
basis_vector_labs[ii])
############################################################
# Plot the Fermi Surface.
# Marching-cubes algorithm is used to find out the isosurface.
############################################################
for ispin in range(self.nspin):
for ii in range(len(self.fermi_xbands[ispin])):
# the band energies in the uc [0, 1]
b3d = self.fermi_ebands3d_uc[ispin][ii]
if cell == 'bz':
# expand the band energies to double uc, [-1, 1]
b3d_2uc = np.tile(b3d, (2, 2, 2))
nx, ny, nz = b3d_2uc.shape
# https://scikit-image.org/docs/stable/api/skimage.measure.html#skimage.measure.marching_cubes_lewiner
verts, faces, normals, values = marching_cubes(b3d_2uc,
level=self.efermi,
spacing=(
2*b1/nx, 2*b2/ny, 2*b3/nz)
)
verts_cart = np.dot(
verts / np.array([b1, b2, b3]) - np.ones(3),
bcell
)
# the region id of the vertices
verts_region_id = tree.query(verts_cart)[1]
# whether the k-points are in BZ?
verts_in_bz = (verts_region_id == gamma_region_id)
# find out the triangles with all vertices inside BZ
verts_cart_fs = verts_cart[faces][
np.alltrue(verts_in_bz[faces], axis=1)
]
else:
nx, ny, nz = b3d.shape
# make band energies periodic in primitive cell
# b3d = np.tile(b3d, (2,2,2))[:nx+1, :ny+1, :nz+1]
b3d = np.pad(b3d, (0,1), mode='wrap') # mayby a little faster?
# https://scikit-image.org/docs/stable/api/skimage.measure.html#skimage.measure.marching_cubes_lewiner
verts, faces, normals, values = marching_cubes(b3d,
level=self.efermi,
spacing=(
b1/nx, b2/ny, b3/nz)
)
verts_cart_fs = np.dot(
verts / np.array([b1, b2, b3]),
bcell
)[faces]
cc = np.linalg.norm(np.sum(verts_cart_fs, axis=1), axis=1)
nn = mpl.colors.Normalize(vmin=cc.min(), vmax=cc.max())
art = Poly3DCollection(verts_cart_fs, facecolor='r',
alpha=0.8, color=mpl.cm.get_cmap(cmap)(nn(cc)))
# art.set_edgecolor('k')
ax.add_collection3d(art)
############################################################
# Plot the Brillouin Zone
############################################################
# The BZ outlines
for xx in l:
ax.plot(xx[:, 0], xx[:, 1], xx[:, 2], color='k', lw=1.0)
# art = Poly3DCollection(f, facecolor='k', alpha=0.1)
# ax.add_collection3d(art)
############################################################
if cell == 'bz':
ax.set_xlim(-b1, b1)
ax.set_ylim(-b2, b2)
ax.set_zlim(-b3, b3)
else:
ax.set_xlim(0, b1)
ax.set_ylim(0, b2)
ax.set_zlim(0, b3)
ax.set_title('Fermi Energy: {:.4f} eV'.format(self.efermi),
fontsize='small')
# plt.tight_layout()
plt.savefig(savefig, dpi=480)
plt.show()
############################################################
elif plot.lower() == 'mayavi':
from mayavi import mlab
# from tvtk.tools import visual
fig = mlab.figure(size=(800, 800))
# visual.set_viewer(fig)
# for b in bcell:
# x, y, z = b
# ar1 = visual.Arrow(x=y, y=y, z=z)
# arrow_length = np.linalg.norm(b)
# ar1.actor.scale=[arrow_length, arrow_length, arrow_length]
# ar1.pos = ar1.pos/arrow_length
# ar1.axis = [x, y, z]
############################################################
# Plot the Brillouin Zone
############################################################
bz_line_width = b1 / 200
# The BZ outlines
for xx in l:
mlab.plot3d(xx[:, 0], xx[:, 1], xx[:, 2],
tube_radius=bz_line_width,
color=(0, 0, 0))
############################################################
# Plot the Fermi Surface.
# Marching-cubes algorithm is used to find out the isosurface.
############################################################
for ispin in range(self.nspin):
for ii in range(len(self.fermi_xbands[ispin])):
# the band energies in the uc [0, 1]
b3d = self.fermi_ebands3d_uc[ispin][ii]
if cell == 'bz':
# expand the band energies to double uc, [-1, 1]
b3d_2uc = np.tile(b3d, (2, 2, 2))
nx, ny, nz = b3d_2uc.shape
# https://scikit-image.org/docs/stable/api/skimage.measure.html#skimage.measure.marching_cubes_lewiner
verts, faces, normals, values = marching_cubes(b3d_2uc,
level=self.efermi,
spacing=(
2*b1/nx, 2*b2/ny, 2*b3/nz)
)
verts_cart = np.dot(
verts / np.array([b1, b2, b3]) - np.ones(3),
bcell
)
# the region id of the vertices
verts_region_id = tree.query(verts_cart)[1]
# whether the k-points are in BZ?
verts_in_bz = (verts_region_id == gamma_region_id)
# find out the triangles with all vertices inside BZ
faces_in_fs = faces[np.all(verts_in_bz[faces], axis=1)]
# keeps the vertices on the Fermi surface and remove all
# the other vertices
vertices_old_id = np.unique(faces_in_fs)
vertices_new_id = range(vertices_old_id.size)
old_new_map = dict(np.c_[vertices_old_id, vertices_new_id])
verts_cart = verts_cart[vertices_old_id]
faces_in_fs = [[old_new_map[v] for v in f] for f in faces_in_fs]
else:
nx, ny, nz = b3d.shape
# make band energies periodic in primitive cell
# b3d = np.tile(b3d, (2,2,2))[:nx+1, :ny+1, :nz+1]
b3d = np.pad(b3d, (0,1), mode='wrap') # mayby a little faster?
# https://scikit-image.org/docs/stable/api/skimage.measure.html#skimage.measure.marching_cubes_lewiner
verts, faces_in_fs, normals, values = marching_cubes(b3d,
level=self.efermi,
spacing=(
b1/nx, b2/ny, b3/nz)
)
verts_cart = np.dot(
verts / np.array([b1, b2, b3]),
bcell
)
# cc = np.linalg.norm(np.sum(verts_cart[faces_in_fs], axis=1), axis=1)
# kk = np.linalg.norm(verts_cart, axis=1)
# print(cc.min(), cc.max())
# print(kk.min(), kk.max())
mlab.triangular_mesh(verts_cart[:,0], verts_cart[:,1], verts_cart[:,2],
faces_in_fs,
colormap='rainbow',
opacity=1.0,
scalars=np.linalg.norm(verts_cart, axis=1),
# vmin=cc.min(), vmax=cc.max()
)
mlab.orientation_axes()
mlab.savefig(savefig)
mlab.show()
else:
raise ValueError("Plotting method should be 'mpl' or 'mayavi'!")
def isosurface_timestep(data,
timestep,
isovalue,
name,
dpi=30,
frame=9,
dx=40,
dy=40,
dz=10,
D=400):
import os
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
from matplotlib import animation
from skimage import measure
nx, ny, nz, nt = shape(data)
if not os.path.exists(name + '_' + str(timestep)):
os.makedirs(name + '_' + str(timestep))
fig = plt.figure(figsize=(30, 30 * 2.5))
ax = fig.add_subplot(111,
projection='3d',
facecolor='w',
label='Inline label')
angle = 0
while (angle <= 360):
percent = np.str(np.round(angle / 360 * 100)) + "%"
print('{}\r'.format(percent), end="")
nameg = name + ' Time:' + str(timestep) + ' Angle:' + str(angle)
vol = data[:, :, :, timestep]
verts, faces, _, _ = measure.marching_cubes_lewiner(vol,
isovalue,
spacing=(dx, dy,
dz))
mesh = Poly3DCollection(verts[faces])
mesh.set_edgecolor('k')
ax.add_collection3d(mesh)
ax.view_init(15, angle)
ax.set_xlabel("X/D", fontsize=50, labelpad=40)
ax.set_ylabel("Y/D", fontsize=50, labelpad=40)
ax.set_zlabel("Z/D", fontsize=50, labelpad=100)
# Title:
namel = len(nameg)
namexpos = 0.5 - 0.01 * namel
ax.text2D(namexpos, 0.85, nameg, transform=ax.transAxes, fontsize=65)
ticnum = 11
ticnumz = 14
xaxis = []
for x in range(np.int(-(ticnum - 1) / 2), np.int((ticnum + 1) / 2)):
xaxis.append(((nx - 1) * dx / (ticnum - 1) * x) / D)
yaxis = []
for y in range(np.int(-(ticnum - 1) / 2), np.int((ticnum - 1) / 2)):
yaxis.append(((ny - 1) * dy / (ticnum - 1) * y) / D)
zaxis = []
for z in range(0, np.int((ticnumz + 1))):
zaxis.append(z * (dz * nz / ticnumz) / D)
ax.set_xticks(np.linspace(0, nx * dx, ticnum))
ax.set_yticks(np.linspace(0, ny * dy, ticnum))
ax.set_xticklabels(xaxis)
ax.set_yticklabels(yaxis)
ax.invert_yaxis()
ax.set_zticks(np.linspace(0, nz * dz, ticnumz + 1))
ax.set_zticklabels(zaxis)
ax.tick_params(axis='both', which='major', labelsize=30)
plt.tight_layout()
filename = name + '_T' + str(timestep) + '/' + name + '_t' + str(
angle) + '.png'
bbox = fig.bbox_inches.from_bounds(1, 9, 28, 58)
plt.savefig(name + '_(' + str(timestep) + ')/' + name + ' ' +
str(angle) + '.png',
bbox_inches=bbox,
dpi=dpi)
plt.cla()
angle = angle + frame
def plotObj3D(prism,
survey,
View_dip,
View_azm,
View_lim,
fig=None,
axs=None,
title=None):
"""
Plot the prism in 3D
"""
x1, x2 = prism.xn[0] - prism.xc, prism.xn[1] - prism.xc
y1, y2 = prism.yn[0] - prism.yc, prism.yn[1] - prism.yc
z1, z2 = prism.zn[0] - prism.zc, prism.zn[1] - prism.zc
pinc, pdec = prism.pinc, prism.pdec
rxLoc = survey.srcField.rxList[0].locs
if fig is None:
fig = plt.figure(figsize=(7, 7))
if axs is None:
axs = fig.add_subplot(111, projection="3d")
if title is not None:
axs.set_title(title)
# plt.rcParams.update({'font.size': 13})
cntr = [prism.x0, prism.y0]
axs.set_xlim3d(-View_lim + cntr[0], View_lim + cntr[0])
axs.set_ylim3d(-View_lim + cntr[1], View_lim + cntr[1])
axs.set_zlim3d(rxLoc[:, 2].max() * 1.1 - View_lim * 2,
rxLoc[:, 2].max() * 1.1)
# Create a rectangular prism, rotate and plot
block_xyz = np.asarray([
[x1, x1, x2, x2, x1, x1, x2, x2],
[y1, y2, y2, y1, y1, y2, y2, y1],
[z1, z1, z1, z1, z2, z2, z2, z2],
])
R = MagUtils.rotationMatrix(pinc, pdec)
xyz = R.dot(block_xyz).T
# Offset the prism to true coordinate
offx = prism.xc
offy = prism.yc
offz = prism.zc
# print xyz
# Face 1
axs.add_collection3d(
Poly3DCollection([
list(zip(xyz[:4, 0] + offx, xyz[:4, 1] + offy, xyz[:4, 2] + offz))
]))
# Face 2
axs.add_collection3d(
Poly3DCollection(
[
list(
zip(xyz[4:, 0] + offx, xyz[4:, 1] + offy,
xyz[4:, 2] + offz))
],
facecolors="w",
))
# Face 3
axs.add_collection3d(
Poly3DCollection([
list(
zip(
xyz[[0, 1, 5, 4], 0] + offx,
xyz[[0, 1, 5, 4], 1] + offy,
xyz[[0, 1, 5, 4], 2] + offz,
))
]))
# Face 4
axs.add_collection3d(
Poly3DCollection([
list(
zip(
xyz[[3, 2, 6, 7], 0] + offx,
xyz[[3, 2, 6, 7], 1] + offy,
xyz[[3, 2, 6, 7], 2] + offz,
))
]))
# Face 5
axs.add_collection3d(
Poly3DCollection([
list(
zip(
xyz[[0, 4, 7, 3], 0] + offx,
xyz[[0, 4, 7, 3], 1] + offy,
xyz[[0, 4, 7, 3], 2] + offz,
))
]))
# Face 6
axs.add_collection3d(
Poly3DCollection([
list(
zip(
xyz[[1, 5, 6, 2], 0] + offx,
xyz[[1, 5, 6, 2], 1] + offy,
xyz[[1, 5, 6, 2], 2] + offz,
))
]))
axs.set_xlabel("East (Y; m)")
axs.set_ylabel("North (X; m)")
axs.set_zlabel("Depth (Z; m)")
axs.scatter(rxLoc[:, 0], rxLoc[:, 1], zs=rxLoc[:, 2], s=1, alpha=0.5)
axs.view_init(View_dip, View_azm)
plt.show()
return True
def display_model(self,
model_info,
model_faces=None,
with_joints=False,
batch_idx=0,
plot=False,
fig=None,
savepath=None):
"""
Displays mesh batch_idx in batch of model_info, model_info as returned by
generate_random_model
"""
if plot:
assert fig is not None
else:
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
verts, joints = model_info['verts'][batch_idx], model_info['joints'][
batch_idx]
if model_faces is None:
ax.scatter(verts[:, 0], verts[:, 1], verts[:, 2], alpha=0.2)
else:
mesh = Poly3DCollection(verts[model_faces],
alpha=0.2) #[model_faces]
face_color = (141 / 255, 184 / 255, 226 / 255)
edge_color = (50 / 255, 50 / 255, 50 / 255)
mesh.set_edgecolor(edge_color)
mesh.set_facecolor(face_color)
ax.add_collection3d(mesh)
if with_joints:
self.draw_skeleton(joints, ax=ax)
#ax.set_xlabel('X')
#ax.set_ylabel('Y')
#ax.set_zlabel('Z')
ax.set_xlim(-0.7, 0.7)
ax.set_ylim(-0.7, 0.7)
ax.set_zlim(-0.7, 0.7)
ax.set_xticks([])
ax.set_yticks([])
ax.set_zticks([])
#ax.get_xaxis().set_ticklabels([])
#ax.get_yaxis().set_ticklabels([])
#ax.set_zticklabels([])
ax.view_init(azim=-90, elev=100)
#for camera
#ax.view_init(azim=-90, elev=10)
fig.subplots_adjust(left=0, right=1, bottom=0, top=1)
if savepath:
print('Saving figure at {}.'.format(savepath))
plt.savefig(savepath, bbox_inches='tight', pad_inches=0)
fig.canvas.draw()
if plot:
return fig
w, h = fig.canvas.get_width_height()
image = np.fromstring(fig.canvas.tostring_rgb(), dtype='uint8')
image = image.reshape([w, h, 3])
plt.close()
return image
def plot_state_city(
state, title="", figsize=None, color=None, alpha=1, ax_real=None, ax_imag=None, *, rho=None
):
"""Plot the cityscape of quantum state.
Plot two 3d bar graphs (two dimensional) of the real and imaginary
part of the density matrix rho.
Args:
state (Statevector or DensityMatrix or ndarray): an N-qubit quantum state.
title (str): a string that represents the plot title
figsize (tuple): Figure size in inches.
color (list): A list of len=2 giving colors for real and
imaginary components of matrix elements.
alpha (float): Transparency value for bars
ax_real (matplotlib.axes.Axes): An optional Axes object to be used for
the visualization output. If none is specified a new matplotlib
Figure will be created and used. If this is specified without an
ax_imag only the real component plot will be generated.
Additionally, if specified there will be no returned Figure since
it is redundant.
ax_imag (matplotlib.axes.Axes): An optional Axes object to be used for
the visualization output. If none is specified a new matplotlib
Figure will be created and used. If this is specified without an
ax_real only the imaginary component plot will be generated.
Additionally, if specified there will be no returned Figure since
it is redundant.
Returns:
matplotlib.Figure:
The matplotlib.Figure of the visualization if the
``ax_real`` and ``ax_imag`` kwargs are not set
Raises:
MissingOptionalLibraryError: Requires matplotlib.
ValueError: When 'color' is not a list of len=2.
VisualizationError: if input is not a valid N-qubit state.
Example:
.. jupyter-execute::
from qiskit import QuantumCircuit
from qiskit.quantum_info import DensityMatrix
from qiskit.visualization import plot_state_city
%matplotlib inline
qc = QuantumCircuit(2)
qc.h(0)
qc.cx(0, 1)
state = DensityMatrix.from_instruction(qc)
plot_state_city(state, color=['midnightblue', 'midnightblue'],
title="New State City")
"""
if not HAS_MATPLOTLIB:
raise MissingOptionalLibraryError(
libname="Matplotlib",
name="plot_state_city",
pip_install="pip install matplotlib",
)
from matplotlib import get_backend
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
rho = DensityMatrix(state)
num = rho.num_qubits
if num is None:
raise VisualizationError("Input is not a multi-qubit quantum state.")
# get the real and imag parts of rho
datareal = np.real(rho.data)
dataimag = np.imag(rho.data)
# get the labels
column_names = [bin(i)[2:].zfill(num) for i in range(2 ** num)]
row_names = [bin(i)[2:].zfill(num) for i in range(2 ** num)]
lx = len(datareal[0]) # Work out matrix dimensions
ly = len(datareal[:, 0])
xpos = np.arange(0, lx, 1) # Set up a mesh of positions
ypos = np.arange(0, ly, 1)
xpos, ypos = np.meshgrid(xpos + 0.25, ypos + 0.25)
xpos = xpos.flatten()
ypos = ypos.flatten()
zpos = np.zeros(lx * ly)
dx = 0.5 * np.ones_like(zpos) # width of bars
dy = dx.copy()
dzr = datareal.flatten()
dzi = dataimag.flatten()
if color is None:
color = ["#648fff", "#648fff"]
else:
if len(color) != 2:
raise ValueError("'color' must be a list of len=2.")
if color[0] is None:
color[0] = "#648fff"
if color[1] is None:
color[1] = "#648fff"
if ax_real is None and ax_imag is None:
# set default figure size
if figsize is None:
figsize = (15, 5)
fig = plt.figure(figsize=figsize)
ax1 = fig.add_subplot(1, 2, 1, projection="3d")
ax2 = fig.add_subplot(1, 2, 2, projection="3d")
elif ax_real is not None:
fig = ax_real.get_figure()
ax1 = ax_real
ax2 = ax_imag
else:
fig = ax_imag.get_figure()
ax1 = None
ax2 = ax_imag
max_dzr = max(dzr)
min_dzr = min(dzr)
min_dzi = np.min(dzi)
max_dzi = np.max(dzi)
if ax1 is not None:
fc1 = generate_facecolors(xpos, ypos, zpos, dx, dy, dzr, color[0])
for idx, cur_zpos in enumerate(zpos):
if dzr[idx] > 0:
zorder = 2
else:
zorder = 0
b1 = ax1.bar3d(
xpos[idx],
ypos[idx],
cur_zpos,
dx[idx],
dy[idx],
dzr[idx],
alpha=alpha,
zorder=zorder,
)
b1.set_facecolors(fc1[6 * idx : 6 * idx + 6])
xlim, ylim = ax1.get_xlim(), ax1.get_ylim()
x = [xlim[0], xlim[1], xlim[1], xlim[0]]
y = [ylim[0], ylim[0], ylim[1], ylim[1]]
z = [0, 0, 0, 0]
verts = [list(zip(x, y, z))]
pc1 = Poly3DCollection(verts, alpha=0.15, facecolor="k", linewidths=1, zorder=1)
if min(dzr) < 0 < max(dzr):
ax1.add_collection3d(pc1)
ax1.set_xticks(np.arange(0.5, lx + 0.5, 1))
ax1.set_yticks(np.arange(0.5, ly + 0.5, 1))
if max_dzr != min_dzr:
ax1.axes.set_zlim3d(np.min(dzr), max(np.max(dzr) + 1e-9, max_dzi))
else:
if min_dzr == 0:
ax1.axes.set_zlim3d(np.min(dzr), max(np.max(dzr) + 1e-9, np.max(dzi)))
else:
ax1.axes.set_zlim3d(auto=True)
ax1.get_autoscalez_on()
ax1.w_xaxis.set_ticklabels(row_names, fontsize=14, rotation=45, ha="right", va="top")
ax1.w_yaxis.set_ticklabels(
column_names, fontsize=14, rotation=-22.5, ha="left", va="center"
)
ax1.set_zlabel("Re[$\\rho$]", fontsize=14)
for tick in ax1.zaxis.get_major_ticks():
tick.label.set_fontsize(14)
if ax2 is not None:
fc2 = generate_facecolors(xpos, ypos, zpos, dx, dy, dzi, color[1])
for idx, cur_zpos in enumerate(zpos):
if dzi[idx] > 0:
zorder = 2
else:
zorder = 0
b2 = ax2.bar3d(
xpos[idx],
ypos[idx],
cur_zpos,
dx[idx],
dy[idx],
dzi[idx],
alpha=alpha,
zorder=zorder,
)
b2.set_facecolors(fc2[6 * idx : 6 * idx + 6])
xlim, ylim = ax2.get_xlim(), ax2.get_ylim()
x = [xlim[0], xlim[1], xlim[1], xlim[0]]
y = [ylim[0], ylim[0], ylim[1], ylim[1]]
z = [0, 0, 0, 0]
verts = [list(zip(x, y, z))]
pc2 = Poly3DCollection(verts, alpha=0.2, facecolor="k", linewidths=1, zorder=1)
if min(dzi) < 0 < max(dzi):
ax2.add_collection3d(pc2)
ax2.set_xticks(np.arange(0.5, lx + 0.5, 1))
ax2.set_yticks(np.arange(0.5, ly + 0.5, 1))
if min_dzi != max_dzi:
eps = 0
ax2.axes.set_zlim3d(np.min(dzi), max(np.max(dzr) + 1e-9, np.max(dzi) + eps))
else:
if min_dzi == 0:
ax2.set_zticks([0])
eps = 1e-9
ax2.axes.set_zlim3d(np.min(dzi), max(np.max(dzr) + 1e-9, np.max(dzi) + eps))
else:
ax2.axes.set_zlim3d(auto=True)
ax2.w_xaxis.set_ticklabels(row_names, fontsize=14, rotation=45, ha="right", va="top")
ax2.w_yaxis.set_ticklabels(
column_names, fontsize=14, rotation=-22.5, ha="left", va="center"
)
ax2.set_zlabel("Im[$\\rho$]", fontsize=14)
for tick in ax2.zaxis.get_major_ticks():
tick.label.set_fontsize(14)
ax2.get_autoscalez_on()
fig.suptitle(title, fontsize=16)
if ax_real is None and ax_imag is None:
if get_backend() in ["module://ipykernel.pylab.backend_inline", "nbAgg"]:
plt.close(fig)
return fig
def plotws(b1, b2, b3):
from pylab import figure, show
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
#draw a vector
from matplotlib.patches import FancyArrowPatch
from mpl_toolkits.mplot3d import proj3d
class Arrow3D(FancyArrowPatch):
def __init__(self, xs, ys, zs, *args, **kwargs):
FancyArrowPatch.__init__(self, (0, 0), (0, 0), *args, **kwargs)
self._verts3d = xs, ys, zs
def draw(self, renderer):
xs3d, ys3d, zs3d = self._verts3d
xs, ys, zs = proj3d.proj_transform(xs3d, ys3d, zs3d, renderer.M)
self.set_positions((xs[0], ys[0]), (xs[1], ys[1]))
FancyArrowPatch.draw(self, renderer)
faces_data, points3d = get_BZ(b1, b2, b3)
import json
#print(json.dumps(faces_data))
faces_coords = faces_data['faces']
faces_count = defaultdict(int)
for face in faces_coords:
faces_count[len(face)] += 1
for num_sides in sorted(faces_count.keys()):
print("{} faces: {}".format(num_sides, faces_count[num_sides]))
fig = figure()
ax = fig.add_subplot(111, projection='3d')
ax.add_collection3d(
Poly3DCollection(faces_coords,
linewidth=1,
alpha=0.9,
edgecolor="k",
facecolor="#ccccff"))
#draw origin
ax.scatter([0], [0], [0], color="g", s=100)
axes_length = 1
# Add axes
ax.add_artist(
Arrow3D((0, axes_length), (0, 0), (0, 0),
mutation_scale=20,
lw=2,
arrowstyle="-|>",
color="k"))
ax.add_artist(
Arrow3D((0, 0), (0, axes_length), (0, 0),
mutation_scale=20,
lw=2,
arrowstyle="-|>",
color="k"))
ax.add_artist(
Arrow3D((0, 0), (0, 0), (0, axes_length),
mutation_scale=20,
lw=2,
arrowstyle="-|>",
color="k"))
ax.text(axes_length, 0, 0, 'ex', (1, 0, 0))
ax.text(0, axes_length, 0, 'ey', (1, 0, 0))
ax.text(0, 0, axes_length, 'ez', (1, 0, 0))
# three primitive vectors
ax.add_artist(
Arrow3D((0, b1[0]), (0, b1[1]), (0, b1[2]),
mutation_scale=21,
lw=1,
arrowstyle="-|>",
color="r"))
ax.add_artist(
Arrow3D((0, b2[0]), (0, b2[1]), (0, b2[2]),
mutation_scale=21,
lw=1,
arrowstyle="-|>",
color="r"))
ax.add_artist(
Arrow3D((0, b3[0]), (0, b3[1]), (0, b3[2]),
mutation_scale=21,
lw=1,
arrowstyle="-|>",
color="r"))
ax.text(b1[0], b1[1], b1[2], 'qlat1', (1, 0, 0))
ax.text(b2[0], b2[1], b2[2], 'qlat2', (1, 0, 0))
ax.text(b3[0], b3[1], b3[2], 'qlat3', (1, 0, 0))
##
import sys, re
iii = ''
eee = ''
x = [''] * 3
y = [''] * 3
n = ''
symlfile = 'syml.' + sys.argv[1]
sfile = open(symlfile, 'r').read().split('\n')
# look for nline
# print ('sfile=',sfile)
i = 0
for iline in sfile:
i = i + 1
ilr = re.split('\s+', iline)
n = int(ilr[0])
if (n == 0): break
nline = i - 1
#print( 'nline=',nline)
for iline in sfile:
i = i + 1
#print(i,iline)
ilr = re.split('\s+', iline)
n = int(ilr[0])
if (n == 0): break
x = [float(ilr[i]) for i in range(1, 4)]
y = [float(ilr[i]) for i in range(4, 7)]
iii = ilr[7]
eee = ilr[8]
#print( n,x[0:3],y[0:3],iii,eee)
ax.add_artist(
Arrow3D((x[0], y[0]), (x[1], y[1]), (x[2], y[2]),
mutation_scale=11,
lw=1,
arrowstyle="-|>",
color="g"))
ax.text(x[0], x[1], x[2], iii, (1, 0, 0))
ax.text(y[0], y[1], y[2], eee, (1, 0, 0))
# # # all face vectors.
# for ix in faces_data['triangles_vertices']: #points3d:
# vvv=ix
# #print(vvv)
# #ax.plot((vvv[0],), (vvv[1],), (vvv[2],), "o", color="#ff0000", ms=8, mew=0.5)
# ax.add_artist(Arrow3D((0,vvv[0]),(0,vvv[1]),(0,vvv[2]),
# mutation_scale=1, lw=.5, arrowstyle="-", color="g"))
## Reset limits
# ax.set_xlim(-1,1)
# ax.set_ylim(-1,1)
# ax.set_zlim(-1,1)
ax.axis('off')
# ax.view_init(elev=0, azim=60)
ax.view_init(elev=0, azim=0)
ax.set_aspect('equal')
ax.autoscale(True, axis='both')
show()
fig = plt.figure()
ax = Axes3D(fig)
for roi in ROIs:
# Concat all vertices
x = roi[0];
x = (x - xmin)*dx
y = roi[1];
y = (-y + ymin)*dx
z = roi[2];
z = -z + zmin
z = np.ones(x.shape) * z
verts = [list(zip(x,y,z))]
# Plot polygons
poly = Poly3DCollection(verts)
poly.set_color(None)
poly.set_edgecolor('b')
ax.add_collection3d(poly)
# Use scatter plot to plot vertices
ax.scatter(x,y,z,c='r')
ax.set_xlim(-7.5, 20)
ax.set_ylim(-20, 7.5)
ax.set_zlim(-14,1)
ax.set_xlabel('X')
ax.set_ylabel('Y')
plt.show()
def print_pore(geom, pores, fig=None, axis_bounds=None):
r"""
Print all throats around a given pore or list of pores accepted as [1,2,3,...,n]
e.g geom.print_pore([34,65,99])
Original vertices plus offset vertices used to create faces and
then printed in 3D
To print all pores (n)
pore_range = np.arange(0,n-1,1)
geom.print_pore(pore_range)
"""
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
return_fig = False
if len(pores) > 0:
net_pores = geom.map_pores(geom._net, pores)
centroids = geom["pore.centroid"][pores]
#centroids2 = self["pore.com"][pores]
#for i,pore in enumerate(pores):
# centroids[i]=self["pore.centroid"][pore]
#coords = self._net["pore.coords"][net_pores]
net_throats = geom._net.find_neighbor_throats(pores=net_pores)
#for net_throat in net_throats:
# try:
# throats.append(geom['throat.map'].tolist().index(net_throat))
# except ValueError:
# " Throat not in this geometry "
throats = geom._net.map_throats(geom, net_throats,
return_mapping=True)["target"]
"Can't create volume from one throat"
if len(throats) >= 1:
verts = geom['throat.vertices'][throats]
normals = geom['throat.normal'][throats]
" Get verts in hull order "
ordered_verts = []
for i in range(len(verts)):
vert_2D = tr.rotate_and_chop(verts[i], normals[i], [0, 0, 1])
hull = ConvexHull(vert_2D, qhull_options='QJ Pp')
ordered_verts.append(verts[i][hull.vertices])
offsets = geom['throat.offset_vertices'][throats]
ordered_offs = []
for i in range(len(offsets)):
offs_2D = tr.rotate_and_chop(offsets[i], normals[i], [0, 0, 1])
offs_hull = ConvexHull(offs_2D, qhull_options='QJ Pp')
ordered_offs.append(offsets[i][offs_hull.vertices])
"Get domain extents for setting axis "
if axis_bounds is None:
[xmin, xmax, ymin, ymax, zmin,
zmax] = vertex_dimension(geom._net, pores, parm='minmax')
else:
[xmin, xmax, ymin, ymax, zmin, zmax] = axis_bounds
if fig is None:
fig = plt.figure()
else:
return_fig == True
ax = fig.gca(projection='3d')
outer_items = Poly3DCollection(ordered_verts,
linewidths=1,
alpha=0.2,
zsort='min')
outer_face_colours = [(1, 0, 0, 0.01)]
outer_items.set_facecolor(outer_face_colours)
ax.add_collection(outer_items)
inner_items = Poly3DCollection(ordered_offs,
linewidths=1,
alpha=0.2,
zsort='min')
inner_face_colours = [(0, 0, 1, 0.01)]
inner_items.set_facecolor(inner_face_colours)
ax.add_collection(inner_items)
ax.set_xlim(xmin, xmax)
ax.set_ylim(ymin, ymax)
ax.set_zlim(zmin, zmax)
#ax.scatter(coords[:,0],coords[:,1],coords[:,2])
ax.scatter(centroids[:, 0],
centroids[:, 1],
centroids[:, 2],
c='y')
#ax.scatter(centroids2[:,0],centroids2[:,1],centroids2[:,2],c='g')
plt.show()
else:
print_throat(throats)
else:
print("Please provide pore indices")
if return_fig == True:
return fig
def display_hand_matplot(
mano_blob,
faces,
ax=None,
alpha=0.2,
cam_view=False,
batch_idx=0,
show=True,
):
"""
Displays hand batch_idx in batch of hand_info, hand_info as returned by
generate_random_hand
"""
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
if ax is None:
fig = plt.figure()
ax = fig.add_subplot(111, projection="3d")
verts, joints = mano_blob.verts[batch_idx], mano_blob.joints[batch_idx]
mesh = Poly3DCollection(verts[faces], alpha=alpha)
face_color = (141 / 255, 184 / 255, 226 / 255)
edge_color = (50 / 255, 50 / 255, 50 / 255)
mesh.set_edgecolor(edge_color)
mesh.set_facecolor(face_color)
ax.add_collection3d(mesh)
# region: joint color >>>>>>>
ax.scatter(joints[0, 0], joints[0, 1], joints[0, 2], s=42, color="c", marker="p")
ax.scatter(joints[1, 0], joints[1, 1], joints[1, 2], color="y", marker="s")
ax.scatter(joints[2, 0], joints[2, 1], joints[2, 2], color="y", marker="^")
ax.scatter(joints[3, 0], joints[3, 1], joints[3, 2], color="y", marker="o")
ax.scatter(joints[4, 0], joints[4, 1], joints[4, 2], color="y", marker="*")
ax.scatter(joints[5, 0], joints[5, 1], joints[5, 2], color="r", marker="s")
ax.scatter(joints[6, 0], joints[6, 1], joints[6, 2], color="r", marker="^")
ax.scatter(joints[7, 0], joints[7, 1], joints[7, 2], color="r", marker="o")
ax.scatter(joints[8, 0], joints[8, 1], joints[8, 2], color="r", marker="*")
ax.scatter(joints[9, 0], joints[9, 1], joints[9, 2], color="b", marker="s")
ax.scatter(joints[10, 0], joints[10, 1], joints[10, 2], color="b", marker="^")
ax.scatter(joints[11, 0], joints[11, 1], joints[11, 2], color="b", marker="o")
ax.scatter(joints[12, 0], joints[12, 1], joints[12, 2], color="b", marker="*")
ax.scatter(joints[13, 0], joints[13, 1], joints[13, 2], color="g", marker="s")
ax.scatter(joints[14, 0], joints[14, 1], joints[14, 2], color="g", marker="^")
ax.scatter(joints[15, 0], joints[15, 1], joints[15, 2], color="g", marker="o")
ax.scatter(joints[16, 0], joints[16, 1], joints[16, 2], color="g", marker="*")
ax.scatter(joints[17, 0], joints[17, 1], joints[17, 2], color="m", marker="s")
ax.scatter(joints[18, 0], joints[18, 1], joints[18, 2], color="m", marker="^")
ax.scatter(joints[19, 0], joints[19, 1], joints[19, 2], color="m", marker="o")
ax.scatter(joints[20, 0], joints[20, 1], joints[20, 2], color="m", marker="*")
# endregion <<<<<<<<<<
if cam_view:
ax.view_init(azim=-90.0, elev=-90.0)
cam_equal_aspect_3d(ax, verts.numpy())
if show:
plt.show()
(z_max - z_min) / size])
offsetAOM = np.array([x_min, y_min, z_min])
#Detuining freq
scale = np.array([
2 * (x_max - x_min) / (size - 1), 2 * (y_max - y_min) / (size - 1),
(z_max - z_min) / (size - 1)
])
offset = np.array([2 * x_min - 180, 2 * y_min - 180, z_min])
# Fancy indexing: `verts[faces]` to generate a collection of triangles
params = scale * verts[faces] + offset
paramsAOM = scaleAOM * verts[faces] + offsetAOM
mesh = Poly3DCollection(params)
mesh.set_edgecolor('k')
mesh.set_linewidth(0.1)
ax.add_collection3d(mesh)
ax.set_xlabel(gp.fields[indexes[0][0]])
ax.set_ylabel(gp.fields[indexes[0][1]])
ax.set_zlabel(gp.fields[indexes[0][2]])
ax.set_xlim(x_min * 2 - 180, x_max * 2 - 180)
ax.set_ylim(y_min * 2 - 180, y_max * 2 - 180)
ax.set_zlim(z_min, z_max)
fname = '3dContuour'
pl.savefig(fname + '.eps', bbox_inches='tight')
pl.savefig(fname + '.png', bbox_inches='tight')
x = np.outer(np.cos(u), np.sin(v)) y = np.outer(np.sin(u), np.sin(v)) z = np.outer(np.ones(np.size(u)), np.cos(v)) ax.plot_surface(x, y, z, color='y', alpha=0.1) # plot generator points ax.plot(points[:, 0], points[:, 1], points[:, 2], 'b.') # plot Voronoi vertices ax.plot(sv.vertices[:, 0], sv.vertices[:, 1], sv.vertices[:, 2], 'g.') # indicate Voronoi regions (as Euclidean polygons) for region in sv.regions: random_color = colors.rgb2hex(np.random.rand(3)) polygon = Poly3DCollection([sv.vertices[region]], alpha=1.0) polygon.set_color(random_color) ax.add_collection3d(polygon) plt.show()
def do_3d_projection(self, renderer):
# if not hasattr(renderer, 'use_gl'):
if hasattr(renderer, '_gl_renderer'): return
Poly3DCollection.do_3d_projection(self,renderer)
#loop over them, see Matlab code # for each tri on that face, two loops f = int(sphere_tuples[0][0]) s = int(sphere_tuples[0][1]) t = int(sphere_tuples[0][2]) #quiz: don't use append def extractPoints(data): points = [] for v in data.vertices: q=[None]*3 #preallocation for i in range(3): q[i]=v['point'][i].real points.append(q) return points points = extractPoints(sphere_data) # here (T grows through the loop) T = [] T=[[points[f],points[s],points[t]]] ax.add_collection3d(Poly3DCollection(T)) plt.show()
def plotBoardLocations(self, X, Y, R, t, n_disp_img=1e5):
# Expects X, U, R, t to be lists of arrays, just like u_meas, v_meas
ind_corners = [
0,
self.n_corners_x - 1,
self.n_corners_x * self.n_corners_y - 1,
self.n_corners_x * (self.n_corners_y - 1),
]
s_cam = 0.02
d_cam = 0.05
xyz_cam = [[0, -s_cam, s_cam, s_cam, -s_cam],
[0, -s_cam, -s_cam, s_cam, s_cam],
[0, -d_cam, -d_cam, -d_cam, -d_cam]]
ind_cam = [[0, 1, 2], [0, 2, 3], [0, 3, 4], [0, 4, 1]]
verts_cam = []
for i in range(len(ind_cam)):
verts_cam.append([
zip([xyz_cam[0][j] for j in ind_cam[i]],
[xyz_cam[1][j] for j in ind_cam[i]],
[xyz_cam[2][j] for j in ind_cam[i]])
])
fig = plt.figure('Estimated Chessboard Locations', figsize=(12, 5))
axim = fig.add_subplot(121)
ax3d = fig.add_subplot(122, projection='3d')
boards = []
verts = []
for p in range(self.n_chessboards):
M = []
W = np.column_stack((R[p], t[p]))
for i in range(4):
M_tld = W.dot(
np.array(
[X[p][ind_corners[i]], Y[p][ind_corners[i]], 0, 1]))
if np.sign(M_tld[2]) == 1:
Rz = np.array([[-1, 0, 0], [0, -1, 0], [0, 0, 1]])
M_tld = Rz.dot(M_tld)
M_tld[2] *= -1
M.append(M_tld[0:3])
M = (np.array(M).T).tolist()
verts.append([zip(M[0], M[1], M[2])])
boards.append(Poly3DCollection(verts[p]))
for i, file in enumerate(sorted(os.listdir(self.cal_img_path))):
if i < n_disp_img:
img = cv2.imread(self.cal_img_path + '/' + file, 0)
axim.imshow(img, cmap='gray')
axim.axis('off')
ax3d.clear()
for j in range(len(ind_cam)):
cam = Poly3DCollection(verts_cam[j])
cam.set_alpha(0.2)
cam.set_color('green')
ax3d.add_collection3d(cam)
for p in range(self.n_chessboards):
if p == i:
boards[p].set_alpha(1.0)
boards[p].set_color('blue')
else:
boards[p].set_alpha(0.1)
boards[p].set_color('red')
ax3d.add_collection3d(boards[p])
ax3d.text(verts[p][0][0][0], verts[p][0][0][1],
verts[p][0][0][2], '{0}'.format(p + 1))
plt.show(block=False)
view_max = 0.2
ax3d.set_xlim(-view_max, view_max)
ax3d.set_ylim(-view_max, view_max)
ax3d.set_zlim(-2 * view_max, 0)
ax3d.set_xlabel('X axis')
ax3d.set_ylabel('Y axis')
ax3d.set_zlabel('Z axis')
if i == 0:
ax3d.view_init(azim=90, elev=120)
plt.tight_layout()
fig.canvas.set_window_title(
'Estimated Board Locations (Chessboard {0})'.format(i + 1))
plt.show(block=False)
raw_input('<Hit Enter To Continue>')
def image_plot(pairs, img, name, depth_only):
skeleton = []
fig1 = plt.figure(figsize=(6, 8))
#### image plot
################
ax = fig1.add_subplot(2, 1, 1)
iters2 = 0
for t in pairs.keys():
if pairs[t][-1] == -1:
continue
### only perform for keypoints more than joints
## for very close part, the wrong association can have large disparity diffference
depth = pairs[t][-1][1]
sca_c = 'b'
dist = pairs[t][-1][0]
kp = pairs[t][0].reshape(1, -1)[0]
sks = np.array(COCO_PERSON_SKELETON) - 1
x = kp[0::3]
y = kp[1::3]
v = kp[2::3]
for sk in sks:
if np.all(v[sk] > 0):
plt.plot(x[sk], y[sk], linewidth=0.3, color='r')
plt.plot(x[v > 0],
y[v > 0],
'o',
markersize=2.5,
markerfacecolor=sca_c,
markeredgecolor='k',
markeredgewidth=0.5)
plt.plot(x[v > 1],
y[v > 1],
'o',
markersize=2.5,
markerfacecolor=sca_c,
markeredgecolor='k',
markeredgewidth=0.5)
if depth[depth > 0].var() > 200:
continue
if round(dist, 1) < 12:
plt.text(np.mean(x[x > 0]) - 10,
y[y > 0].min() + 5 * (iters2 - 3),
round(dist, 1),
c='w',
fontsize=10,
weight="bold",
bbox=dict(facecolor='black', alpha=0.5, boxstyle='round'))
else:
plt.text(np.mean(x[x > 0]) - 10,
y[y > 0].min() + 5 * (iters2 - 3),
round(dist, 1),
c='w',
fontsize=6,
weight="bold",
bbox=dict(facecolor='black', alpha=0.5, boxstyle='round'))
iters2 += 1
ax.set_title('left stereo image')
ax.imshow(img)
#### skeleton plot
##################
if not depth_only:
ax = fig1.add_subplot(2, 1, 2, projection='3d')
ax.set_zlabel('y')
ax.set_ylabel('x')
ax.set_xlabel('depth')
ax.set_title('3D Pose')
ax.set_ylim3d(0, img.shape[1])
ax.set_zlim3d(0, img.shape[0])
ax.set_xlim3d(0, 40)
nums = []
iters = 0
for t in pairs.keys():
if pairs[t][-1] == -1:
continue
value = pairs[t][0]
value[:, 2] = pairs[t][-1][1]
Z = np.copy(value)
if len(Z[:, 2][Z[:, 2] > 0]) < 5:
continue
dist = pairs[t][-1][0]
if dist[dist > 0].var() > 200:
nums.append(iters)
iters += 1
continue
Z[:, 2][abs(Z[:, 2] - np.median(Z[:, 2][Z[:, 2] > 0])) > 5] = 0
Z1 = np.copy(Z[Z[:, 2] != 0])
Z1[:, 2][Z1[:, 2] - np.median(Z1[:, 2][Z1[:, 2] > 0]) > 5] = 0
if len(Z1) == 0:
nums.append(iters)
for i in COCO_PERSON_SKELETON:
a, b = i
if Z[a - 1, 2] == 0 or Z[b - 1, 2] == 0:
continue
else:
skeleton.append([[Z[a - 1][2], Z[a - 1][0], Z[a - 1][1]],
[Z[b - 1][2], Z[b - 1][0], Z[b - 1][1]]])
iters += 1
# plot sides
ax.add_collection3d(
Poly3DCollection(skeleton, edgecolors='r', alpha=.25))
ax.scatter(Z1[:, 2], Z1[:, 0], Z1[:, 1], c='b')
# rotate the axes and update
for angle in range(0, 360):
ax.view_init(210, angle)
plt.savefig(name.split('.')[0] + '_result.png')
fig1.canvas.draw()
def plot_power_density_stl(P,
title='Power Density [$W/mm^2$]',
elev=30,
azim=30,
alpha=0.8,
bbox_inches='tight',
transparent=True,
ofile=None,
colorbar=True):
pmax = max([p[1] for p in P])
pmin = min([p[1] for p in P])
m = cm.ScalarMappable(cm.viridis)
#m.set_array([p[1]/pmax for p in P])
xmax = ymax = zmax = -99999
xmin = ymin = zmin = +99999
for p in P:
xmax = max([xmax, p[0][0][0], p[0][1][0], p[0][2][0]])
xmin = min([xmin, p[0][0][0], p[0][1][0], p[0][2][0]])
zmax = max([zmax, p[0][0][1], p[0][1][1], p[0][2][1]])
zmin = min([zmin, p[0][0][1], p[0][1][1], p[0][2][1]])
ymax = max([ymax, p[0][0][2], p[0][1][2], p[0][2][2]])
ymin = min([ymin, p[0][0][2], p[0][1][2], p[0][2][2]])
fig = plt.figure()
ax = Axes3D(fig)
for p in P:
pp = copy.deepcopy(p)
pp[0][0][1] = p[0][0][2]
pp[0][0][2] = p[0][0][1]
pp[0][1][1] = p[0][1][2]
pp[0][1][2] = p[0][1][1]
pp[0][2][1] = p[0][2][2]
pp[0][2][2] = p[0][2][1]
triangle = Poly3DCollection([pp[0]],
alpha=alpha,
edgecolors='b',
linewidths=0.05)
triangle.set_facecolor(m.to_rgba(pp[1] / pmax))
#triangle.set_facecolor([1, 1-p[1]/pmax, 1-p[1]/pmax])
ax.add_collection3d(triangle)
#ax.view_init(elev=elev, azim=azim)
plt.title(title)
ax.invert_xaxis()
ax.set_xlim([xmin, xmax])
ax.set_ylim([ymin, ymax])
ax.set_zlim([zmin, zmax])
ax.set_xlabel('X [m]')
ax.set_ylabel('Z [m]')
ax.set_zlabel('Y [m]')
if colorbar is True:
sm = plt.cm.ScalarMappable(cmap=cm.viridis,
norm=plt.Normalize(vmin=pmin, vmax=pmax))
sm._A = []
plt.colorbar(sm, format='%.0e')
if ofile is not None:
plt.savefig(ofile, bbox_inches=bbox_inches, transparent=transparent)
plt.show()
return
#celda.vor_gal_id(cv[2])
#
vol_void = []
for i in range(len(cv)):
celda.vor_gal_id(cv[i])
vol_void.append(celda.vol)
vol_V = sum(vol_void)
r_void = np.cbrt(3. / 4. / np.pi * vol_V)
#
f = plt.figure(figsize=(8, 6))
ax = f.add_subplot(111, projection='3d')
points = celda.vor_tess.points[cv]
bg = celda.vor_tess.points
ax.plot(points[:, 0], points[:, 1], points[:, 2], 'r+')
ax.plot(bg[:, 0], bg[:, 1], bg[:, 2], 'k.', ms=1.)
for i in range(len(cv)):
celda.vor_gal_id(cv[i])
faces = celda.faces
for j in range(len(faces)):
poli = Poly3DCollection([faces[j]])
poli.set_edgecolor('black')
poli.set_facecolor('red')
ax.add_collection(poli)
plt.show()
def test_nearest_gal_neigh():
for i in range(len(dim2.gals_zobov)):
assert i == dim2.nearest_gal_neigh(dim2.gals_zobov[i],
coordinates='com')
def isosurface(data,
isovalue,
name,
dpi=30,
frame=5,
angleH=15,
angleV=60,
dx=40,
dy=40,
dz=10,
D=400):
import os
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
from matplotlib import animation
from skimage import measure
if not os.path.exists(name):
os.makedirs(name)
nx, ny, nz, nt = shape(data)
t = 0
fig = plt.figure(figsize=(30, 30 * 2.5))
ax = fig.add_subplot(111,
projection='3d',
facecolor='w',
label='Inline label')
while (t < nt):
percent = np.str(np.round(t / nt * 100)) + "%"
print('{}\r'.format(percent), end="")
title_name = name + ' Time:' + str(t)
fr = 0
vol = data[:, :, :, t]
datamax = vol.max()
datamin = vol.min()
while (isovalue >= datamax or isovalue <= datamin):
t = t + 1
fr = fr + 1
if (fr == frame):
fr = 0
vol = data[:, :, :, t]
datamax = vol.max()
datamin = vol.min()
verts, faces, _, _ = measure.marching_cubes_lewiner(vol,
isovalue,
spacing=(dx, dy,
dz))
mesh = Poly3DCollection(verts[faces])
mesh.set_edgecolor('k')
ax.add_collection3d(mesh)
ax.view_init(angleH, angleV)
ax.set_xlabel("X/D", fontsize=50, labelpad=40)
ax.set_ylabel("Y/D", fontsize=50, labelpad=40)
ax.set_zlabel("Z/D", fontsize=50, labelpad=100)
# Title:
namel = len(title_name)
namexpos = 0.5 - 0.01 * namel
ax.text2D(namexpos,
0.85,
title_name,
transform=ax.transAxes,
fontsize=65)
ticnum = 11
ticnumz = 14
xaxis = []
for x in range(np.int(-(ticnum - 1) / 2), np.int((ticnum + 1) / 2)):
xaxis.append(((nx - 1) * dx / (ticnum - 1) * x) / D)
yaxis = []
for y in range(np.int(-(ticnum - 1) / 2), np.int((ticnum - 1) / 2)):
yaxis.append(((ny - 1) * dy / (ticnum - 1) * y) / D)
zaxis = []
for z in range(0, np.int((ticnumz + 1))):
zaxis.append(z * (dz * nz / ticnumz) / D)
ax.set_xticks(np.linspace(0, nx * dx, ticnum))
ax.set_yticks(np.linspace(0, ny * dy, ticnum))
ax.set_xticklabels(xaxis)
ax.set_yticklabels(yaxis)
ax.invert_yaxis()
ax.set_zticks(np.linspace(0, nz * dz, ticnumz + 1))
ax.set_zticklabels(zaxis)
ax.tick_params(axis='both', which='major', labelsize=30)
plt.tight_layout()
bbox = fig.bbox_inches.from_bounds(1, 9, 28, 58)
if (t < 10):
picname = '00' + str(t)
if (t >= 10 and t < 100):
picname = '0' + str(t)
if (t >= 100):
picname = str(t)
filename = name + '/' + picname + '.png'
plt.savefig(filename, bbox_inches=bbox, dpi=dpi)
plt.cla()
if (fr == 0):
fr = frame
else:
fr = frame - fr
t = t + fr
print('Done.')
def print3d_discrete_xy(varx, vary):
fxy_inner = varx + vary + 'inner_joint.out'
fxy_skewed_inner = varx + vary + 'skinner_joint.out'
fxy_skewed_outer = varx + vary + 'skouter_joint.out'
fx_outer2 = varx + 'outer.out'
fy_outer2 = vary + 'outer.out'
fx_inner = varx + 'inner.out'
fy_inner = vary + 'inner.out'
if (path.isfile(fx_outer2) and path.isfile(fy_outer2)):
#fig, ax = plt.subplots(figsize=(width_in_inches, height_in_inches), dpi=dots_per_inch)
fig = plt.figure()
# ax = fig.add_subplot(1, 1, 1, projection='3d')
ax = fig.add_subplot(
111, projection='3d'
) #ax = fig.gca(projection='3d') ##Axes3D(fig) #fig.gca(projection='3d')
plt.grid(True, which="both", linestyle='--')
# rectangles
if (not path.isfile(fxy_skewed_outer)):
with open(fx_outer2, 'r') as x_outer2, open(fy_outer2,
'r') as y_outer2:
linesx_outer2 = x_outer2.readlines()
t1_outer = [float(line.split()[0]) for line in linesx_outer2]
xmin_outer2 = [
float(line.split()[1]) for line in linesx_outer2
]
xmax_outer2 = [
float(line.split()[2]) for line in linesx_outer2
]
linesy_outer2 = y_outer2.readlines()
ymin_outer2 = [
float(line.split()[1]) for line in linesy_outer2
]
ymax_outer2 = [
float(line.split()[2]) for line in linesy_outer2
]
for t1, xo1, xo2, yo1, yo2 in zip(t1_outer, xmin_outer2,
xmax_outer2, ymin_outer2,
ymax_outer2):
Z = np.array([[xo1, t1, yo1], [xo2, t1, yo1],
[xo2, t1, yo2], [xo1, t1, yo2]])
ax.scatter3D(Z[:, 0], Z[:, 1], Z[:, 2])
verts = [[Z[0], Z[1], Z[2], Z[3]]]
ax.add_collection3d(
Poly3DCollection(verts,
facecolors='g',
linewidths=2,
edgecolors='g',
label='maximal inner-approximation',
alpha=.1))
if (path.isfile(fxy_inner) and os.stat(fxy_inner).st_size != 0):
with open(fxy_inner, 'r') as xy_inner:
linesxy_inner = xy_inner.readlines()
t1_inner = [float(line.split()[0]) for line in linesxy_inner]
xmin_inner = [float(line.split()[1]) for line in linesxy_inner]
xmax_inner = [float(line.split()[2]) for line in linesxy_inner]
ymin_inner = [float(line.split()[3]) for line in linesxy_inner]
ymax_inner = [float(line.split()[4]) for line in linesxy_inner]
for t1, xi1, xi2, yi1, yi2 in zip(t1_inner, xmin_inner,
xmax_inner, ymin_inner,
ymax_inner):
Z = np.array([[xi1, t1, yi1], [xi2, t1, yi1],
[xi2, t1, yi2], [xi1, t1, yi2]])
ax.scatter3D(Z[:, 0], Z[:, 1], Z[:, 2])
verts = [[Z[0], Z[1], Z[2], Z[3]]]
ax.add_collection3d(
Poly3DCollection(verts,
facecolors='orange',
linewidths=2,
linestyle='--',
edgecolors='b',
label='maximal inner-approximation',
alpha=.3))
# skew box
if (path.isfile(fxy_skewed_outer)):
with open(fxy_skewed_outer, 'r') as xy_skewed_outer:
linesxy_skewed_outer = xy_skewed_outer.readlines()
t1_outer = [
float(line.split()[0]) for line in linesxy_skewed_outer
]
x1_outer = [
float(line.split()[1]) for line in linesxy_skewed_outer
]
y1_outer = [
float(line.split()[2]) for line in linesxy_skewed_outer
]
x2_outer = [
float(line.split()[3]) for line in linesxy_skewed_outer
]
y2_outer = [
float(line.split()[4]) for line in linesxy_skewed_outer
]
x3_outer = [
float(line.split()[5]) for line in linesxy_skewed_outer
]
y3_outer = [
float(line.split()[6]) for line in linesxy_skewed_outer
]
x4_outer = [
float(line.split()[7]) for line in linesxy_skewed_outer
]
y4_outer = [
float(line.split()[8]) for line in linesxy_skewed_outer
]
patches = []
for t1, xi1, yi1, xi2, yi2, xi3, yi3, xi4, yi4 in zip(
t1_outer, x1_outer, y1_outer, x2_outer, y2_outer,
x3_outer, y3_outer, x4_outer, y4_outer):
Z = np.array([[xi1, t1, yi1], [xi2, t1, yi2],
[xi3, t1, yi3], [xi4, t1, yi4]])
# plot vertices
ax.scatter3D(Z[:, 0], Z[:, 1], Z[:, 2])
# list of sides' polygons of figure
verts = [[Z[0], Z[1], Z[2], Z[3]]]
ax.add_collection3d(
Poly3DCollection(verts,
facecolors='g',
linewidths=2,
edgecolors='g',
label='maximal inner-approximation',
alpha=.1))
if (path.isfile(fxy_skewed_inner)):
with open(fxy_skewed_inner, 'r') as xy_skewed_inner:
linesxy_skewed_inner = xy_skewed_inner.readlines()
t1_inner = [
float(line.split()[0]) for line in linesxy_skewed_outer
]
x1_inner = [
float(line.split()[1]) for line in linesxy_skewed_inner
]
y1_inner = [
float(line.split()[2]) for line in linesxy_skewed_inner
]
x2_inner = [
float(line.split()[3]) for line in linesxy_skewed_inner
]
y2_inner = [
float(line.split()[4]) for line in linesxy_skewed_inner
]
x3_inner = [
float(line.split()[5]) for line in linesxy_skewed_inner
]
y3_inner = [
float(line.split()[6]) for line in linesxy_skewed_inner
]
x4_inner = [
float(line.split()[7]) for line in linesxy_skewed_inner
]
y4_inner = [
float(line.split()[8]) for line in linesxy_skewed_inner
]
for t1, xi1, yi1, xi2, yi2, xi3, yi3, xi4, yi4 in zip(
t1_inner, x1_inner, y1_inner, x2_inner, y2_inner,
x3_inner, y3_inner, x4_inner, y4_inner):
Z = np.array([[xi1, t1, yi1], [xi2, t1, yi2],
[xi3, t1, yi3], [xi4, t1, yi4]])
# plot vertices
ax.scatter3D(Z[:, 0], Z[:, 1], Z[:, 2])
# list of sides' polygons of figure
verts = [[Z[0], Z[1], Z[2], Z[3]]]
ax.add_collection3d(
Poly3DCollection(verts,
facecolors='orange',
linewidths=2,
linestyle='--',
edgecolors='b',
label='maximal inner-approximation',
alpha=.3))
if (path.isfile('xi.out')):
with open('xi.out', 'r') as xi:
lines_xi = xi.readlines()
t = [float(line.split()[0]) for line in lines_xi]
z1 = [float(line.split()[1]) for line in lines_xi]
z2 = [float(line.split()[2]) for line in lines_xi]
# ax.scatter3D(z1,t,z2,c='purple',alpha=1.,s=1.,label='estimated reachable states')
ax.autoscale()
ax.set_xlabel(varx, fontsize="x-large")
ax.set_zlabel(vary, fontsize="x-large")
ax.set_ylabel('step', fontsize="x-large")
ax.xaxis.set_major_locator(mticker.MaxNLocator(5))
ax.zaxis.set_major_locator(mticker.MaxNLocator(5))
# ax.set_zlim3d(0, 25)
# plt.legend(fontsize="x-large",loc='center')
# plt.legend(fontsize="x-large",loc='lower right')
f_output = varx + vary + 'time'
plt.savefig(f_output)
plt.show()
plt.close()
print xn,yn
#custom draw surface
poly3d = np.zeros((xn*(yn-1), 4, 3))
for yk in range(yn-1):
for xk in range(xn):
itr = yk*xn+xk
if xk==xn-1:
poly3d[itr,:,:] = [[X[xk, yk] , Y[xk, yk] , W[xk, yk] ],
[X[0, yk] , Y[0, yk] , W[0, yk] ],
[X[0, yk+1] , Y[0, yk+1] , W[0, yk+1] ],
[X[xk, yk+1] , Y[xk, yk+1] , W[xk, yk+1]]]
else:
poly3d[itr,:,:] = [[X[xk, yk] , Y[xk, yk] , W[xk, yk] ],
[X[xk+1, yk] , Y[xk+1, yk] , W[xk+1, yk] ],
[X[xk+1, yk+1] , Y[xk+1, yk+1] , W[xk+1, yk+1]],
[X[xk, yk+1] , Y[xk, yk+1] , W[xk, yk+1] ]]
plt.xlim(-2.1,2.1)
plt.ylim(-2.1,2.1)
ax.add_collection3d(Poly3DCollection(poly3d, facecolors='#77dd77', linewidths=1,alpha=.5))
ax.add_collection3d(Line3DCollection(poly3d, colors='k', linewidths=.2))
#ax.plot_surface(X, Y, W, rstride=1, cstride=1, cmap=cm.jet)
#ax.plot_wireframe(X, Y, W, rstride=5, cstride=5)
#ax.contourf(X, Y, W, zdir='z', offset=-1, cmap=cm.coolwarm)
plt.show()
Z = clf.decision_function(np.c_[xx.ravel(), yy.ravel(), zz.ravel()])
Z = Z.reshape(xx.shape)
plt.title("Novelty Detection")
ax = plt.gca(projection='3d')
b1 = ax.scatter(X_train[:, 0], X_train[:, 1], X_train[:, 2], c='white')
b2 = ax.scatter(X_test[:, 0], X_test[:, 1], X_test[:, 2], c='green')
c = ax.scatter(X_outliers[:, 0], X_outliers[:, 1], X_outliers[:, 2], c='red')
verts, faces = measure.marching_cubes(Z, 0)
verts = verts * \
[X_MAX - X_MIN, Y_MAX - Y_MIN, Z_MAX - Z_MIN] / SPACE_SAMPLING_POINTS
verts = verts + [X_MIN, Y_MIN, Z_MIN]
mesh = Poly3DCollection(verts[faces],
facecolor='orange',
edgecolor='gray',
alpha=0.3)
ax.add_collection3d(mesh)
ax.set_xlim((-10, 10))
ax.set_ylim((-10, 10))
ax.set_zlim((-10, 10))
ax.axis('tight')
ax.set_xlabel("X")
ax.set_ylabel("Y")
ax.set_zlabel("Z")
ax.legend([mpatches.Patch(color='orange', alpha=0.3), b1, b2, c], [
"learned frontier", "training observations", "new regular observations",
"new abnormal observations"
],
def plot3d_anim(times, states, modes, ps_list, Nz_list, skip=1, filename=None):
'''
make a 3d plot of the GCAS maneuver
'''
full_plot = True
if filename == '': # plot to the screen
filename = None
skip = 20
full_plot = False
elif filename.endswith('.gif'):
skip = 5
else:
skip = 1 # plot every frame
assert len(times) == len(states)
start = time.time()
times = times[0::skip]
states = states[0::skip]
modes = modes[0::skip]
ps_list = ps_list[0::skip]
Nz_list = Nz_list[0::skip]
fig = plt.figure(figsize=(6, 5))
ax = fig.add_subplot(111, projection='3d')
ax.view_init(30, 45)
pos_xs = [pt[9] for pt in states]
pos_ys = [pt[10] for pt in states]
pos_zs = [pt[11] for pt in states]
trail_line, = ax.plot([], [], [], color='r', lw=1)
data = loadmat('f-16.mat')
f16_pts = data['V']
f16_faces = data['F']
plane_polys = Poly3DCollection([], color=None if full_plot else 'k')
ax.add_collection3d(plane_polys)
ax.set_xlim([min(pos_xs), max(pos_xs)])
ax.set_ylim([min(pos_ys), max(pos_xs)])
ax.set_zlim([min(pos_zs), max(pos_zs)])
ax.set_xlabel('X [ft]')
ax.set_ylabel('Y [ft]')
ax.set_zlabel('Altitude [ft] ')
frames = len(times)
# text
fontsize = 14
time_text = ax.text2D(0.05,
1.07,
"",
transform=ax.transAxes,
fontsize=fontsize)
mode_text = ax.text2D(0.95,
1.07,
"",
transform=ax.transAxes,
fontsize=fontsize,
horizontalalignment='right')
alt_text = ax.text2D(0.05,
1.00,
"",
transform=ax.transAxes,
fontsize=fontsize)
v_text = ax.text2D(0.95,
1.00,
"",
transform=ax.transAxes,
fontsize=fontsize,
horizontalalignment='right')
alpha_text = ax.text2D(0.05,
0.93,
"",
transform=ax.transAxes,
fontsize=fontsize)
beta_text = ax.text2D(0.95,
0.93,
"",
transform=ax.transAxes,
fontsize=fontsize,
horizontalalignment='right')
nz_text = ax.text2D(0.05,
0.86,
"",
transform=ax.transAxes,
fontsize=fontsize)
ps_text = ax.text2D(0.95,
0.86,
"",
transform=ax.transAxes,
fontsize=fontsize,
horizontalalignment='right')
ang_text = ax.text2D(0.5,
0.79,
"",
transform=ax.transAxes,
fontsize=fontsize,
horizontalalignment='center')
def anim_func(frame):
'updates for the animation frame'
print("{}/{}".format(frame, frames))
speed = states[frame][0]
alpha = states[frame][1]
beta = states[frame][2]
alt = states[frame][11]
phi = states[frame][3]
theta = states[frame][4]
psi = states[frame][5]
dx = states[frame][9]
dy = states[frame][10]
dz = states[frame][11]
time_text.set_text('t = {:.2f} sec'.format(times[frame]))
colorMap = {GcasAutopilot.STATE_START:'red', GcasAutopilot.STATE_ROLL: 'blue', \
GcasAutopilot.STATE_PULL:'green', GcasAutopilot.STATE_DONE:'magenta'}
mode = modes[frame]
col = colorMap[mode]
mode_text.set_color(col)
mode_text.set_text('Mode: {}'.format(mode))
alt_text.set_text('h = {:.2f} ft'.format(alt))
v_text.set_text('V = {:.2f} ft/sec'.format(speed))
alpha_text.set_text('$\\alpha$ = {:.2f} deg'.format(rad2deg(alpha)))
beta_text.set_text('$\\beta$ = {:.2f} deg'.format(rad2deg(beta)))
nz_text.set_text('$N_z$ = {:.2f} g'.format(Nz_list[frame]))
ps_text.set_text('$p_s$ = {:.2f} deg/sec'.format(
rad2deg(ps_list[frame])))
ang_text.set_text('[$\\phi$, $\\theta$, $\\psi$] = [{:.2f}, {:.2f}, {:.2f}] deg'.format(\
rad2deg(phi), rad2deg(theta), rad2deg(psi)))
# do trail
trail_len = 200 / skip
start_index = max(0, frame - trail_len)
trail_line.set_data(pos_xs[start_index:frame],
pos_ys[start_index:frame])
trail_line.set_3d_properties(pos_zs[start_index:frame])
scale = 25
pts = scale3d(f16_pts, [-scale, scale, scale])
pts = rotate3d(pts, theta, -psi, phi)
size = 1000
minx = dx - size
maxx = dx + size
miny = dy - size
maxy = dy + size
minz = dz - size
maxz = dz + size
ax.set_xlim([minx, maxx])
ax.set_ylim([miny, maxy])
ax.set_zlim([minz, maxz])
verts = []
fc = []
count = 0
for face in f16_faces:
face_pts = []
count = count + 1
if not full_plot and count % 10 != 0:
continue
for index in face:
face_pts.append((pts[index-1][0] + dx, \
pts[index-1][1] + dy, \
pts[index-1][2] + dz))
verts.append(face_pts)
fc.append('k')
# draw ground
if minz <= 0 and maxz >= 0:
z = 0
verts.append([(minx, miny, z), (maxx, miny, z), (maxx, maxy, z),
(minx, maxy, z)])
fc.append('0.8')
plane_polys.set_verts(verts)
plane_polys.set_facecolors(fc)
return None
anim_obj = animation.FuncAnimation(fig, anim_func, frames, interval=30, \
blit=False, repeat=True)
if filename is not None:
if filename.endswith('.gif'):
print "\nSaving animation to '{}' using 'imagemagick'...".format(
filename)
anim_obj.save(filename, dpi=80, writer='imagemagick')
print "Finished saving to {} in {:.1f} sec".format(
filename,
time.time() - start)
else:
fps = 60
codec = 'libx264'
print "\nSaving '{}' at {:.2f} fps using ffmpeg with codec '{}'.".format(
filename, fps, codec)
# if this fails do: 'sudo apt-get install ffmpeg'
try:
extra_args = []
if codec is not None:
extra_args += ['-vcodec', str(codec)]
anim_obj.save(filename, fps=fps, extra_args=extra_args)
print "Finished saving to {} in {:.1f} sec".format(
filename,
time.time() - start)
except AttributeError:
traceback.print_exc()
print "\nSaving video file failed! Is ffmpeg installed? Can you run 'ffmpeg' in the terminal?"
else:
plt.show()
def createPics(tracks):
fontfile = os.path.join(os.path.dirname(__file__), 'Fonts/FreeSans.ttf')
randFilename = random.randrange(0, 100001, 2)
#PIL_images_dir = os.path.join(os.path.dirname(__file__) , 'tmp/')
profile_filename = 'tmp/profile' + str(randFilename)
# serialize tracks
track = []
for t in tracks:
track.extend(t)
"""
# set scales:
maxDist=track[len(track)-1]['dist']
minEle=track[0]['ele']
maxEle=track[0]['ele']
for t in track:
if t['ele'] !=0: # discontinuities
if t['ele'] < minEle: minEle=t['ele']
if t['ele'] > maxEle: maxEle=t['ele']
# Set format
maxDistValue=" %.1fkm" % maxDist
minEleValue=" %.fm" % minEle
maxEleValue=" %.fm" % maxEle
minLat=track[0]['lat']
maxLat=track[0]['lat']
for t in track:
if t['ele'] !=0: # discontinuities
if t['lat'] < minLat: minLat=t['lat']
if t['lat'] > maxLat: maxLat=t['lat']
minLon=track[0]['lon']
maxLon=track[0]['lon']
for t in track:
if t['ele'] !=0: # discontinuities
if t['lon'] < minLon: minLon=t['lon']
if t['lon'] > maxLon: maxLon=t['lon']
# Set markers near the track fourth
#~ markers=[]
#~ for i in range(1, len(track)):
#~ if track[i-1]['dist'] < maxDist/4 and track[i]['dist'] > maxDist/4:
#~ markers.append(track[i])
#~ if track[i-1]['dist'] < maxDist/2 and track[i]['dist'] > maxDist/2:
#~ markers.append(track[i])
#~ if track[i-1]['dist'] < maxDist*3/4 and track[i]['dist'] > maxDist*3/4:
#~ markers.append(track[i])
# Set the route points
points=[]
for t in tracks:
points.append(t[-1])
points=points[:-1]
# Provide a reasonable scale for flat tracks
if (maxEle - minEle) < 50:
maxEle = (maxEle + minEle)/2 + 25
minEle = (maxEle + minEle)/2 - 25
#---------------------------------------------
#------- draw the elevation profile ----------
#---------------------------------------------
# All sizes are *2 then we downsample for aliasing
sans=ImageFont.truetype(fontfile,10*2)
#sans=ImageFont.truetype('FreeSans.ttf',10*2) # XX
width=250*2
height=120*2
margin=15
marginLeft=sans.getsize(str(maxEleValue))[0]
marginBottom=sans.getsize(str(maxDistValue))[1]
plotHeight=height-2*margin-marginBottom
plotWidth=width-2*margin-marginLeft
im = Image.new('RGB',(width,height),'#FFFFFF')
draw = ImageDraw.Draw(im)
#Draw plot
# draw elevation grid (20m)
for i in range(int(minEle/20), int(maxEle/20)+1):
if i*20 > minEle and i*20< maxEle:
x1=margin+marginLeft
y =height-marginBottom-(i*20-minEle)/(maxEle-minEle)*plotHeight
x2=width-margin
draw.line((x1,y,x2,y),fill='#BBBBBB',width=1)
# draw profile
for i in range(1, len(track)):
x1=margin+marginLeft+track[i-1]['dist']/maxDist*plotWidth
y1=height-marginBottom-(track[i-1]['ele']-minEle)/(maxEle-minEle)*plotHeight
x2=margin+marginLeft+track[i]['dist']/maxDist*plotWidth
y2=height-marginBottom-(track[i]['ele']-minEle)/(maxEle-minEle)*plotHeight
if track[i]['ele'] == 0 or track[i-1]['ele'] == 0:
# discontinuities
draw.line((x1,y1,x2,y2),fill='#606060',width=1)
else:
draw.line((x1,y1,x2,y2),fill='#808080',width=3)
# Draw point at start, end
r = 15
x1=margin+marginLeft+track[0]['dist']/maxDist*plotWidth
y1=height-marginBottom-(track[0]['ele']-minEle)/(maxEle-minEle)*plotHeight
x2=margin+marginLeft+track[len(track)-1]['dist']/maxDist*plotWidth
y2=height-marginBottom-(track[len(track)-1]['ele']-minEle)/(maxEle-minEle)*plotHeight
draw.ellipse((x1-r/2,y1-r/2,x1+r/2,y1+r/2), fill='#AAAAAA', outline='#000000')
draw.ellipse((x2-r/2,y2-r/2,x2+r/2,y2+r/2), fill='#000000')
# Draw points on route points
r = 8
for point in points:
x1=margin+marginLeft+point['dist']/maxDist*plotWidth
y1=height-marginBottom-(point['ele']-minEle)/(maxEle-minEle)*plotHeight
draw.ellipse((x1-r/2,y1-r/2,x1+r/2,y1+r/2), fill='#FFFFFF', outline='#000000')
# draw a white rectangle under the scales:
x = 0
y = height-marginBottom +2
draw.rectangle((x,y,width,height),\
fill='#EEEEEE', outline='#EEEEEE')
draw.rectangle((0,0,marginLeft,height),\
fill='#EEEEEE', outline='#EEEEEE')
# Draw scales:
#~ draw.text((margin+marginLeft,height-marginBottom),'0',fill='#000000',font=sans)
#~ draw.text((width-sans.getsize(str(maxDistValue))[0],\
#~ height-marginBottom),str(maxDistValue),fill='#000000',font=sans)
draw.text((2,height-marginBottom - sans.getsize('1')[1]/2),minEleValue,fill='#000000',font=sans)
draw.text((2,\
height-marginBottom-plotHeight - sans.getsize('1')[1]/2),maxEleValue,fill='#000000',font=sans)
#Draw markers
#~ for m in markers:
#~ mDist=" %.1fkm" % m['dist']
#~ x=margin+marginLeft+m['dist']/maxDist*plotWidth\
#~ -sans.getsize(str(m['dist']))[0]/2
#~ y=height-marginBottom
#~ draw.text((x,y),mDist,fill='#000000',font=sans)
del draw
resolution=(int(width/2),int(height/2))
im = im.resize(resolution,Image.ANTIALIAS)
outname=PIL_images_dir + profile_filename
im.save(outname, "PNG")
"""
lats = []
lons = []
eles = []
dists = []
for t in tracks:
lats.append(t['lat'])
lons.append(t['lon'])
eles.append(t['ele'])
dists.append(t['dist'])
#~ plt.plot(lons,lats)
#~ plt.show()
#~ fig = plt.figure()
#~ ax = fig.gca(projection='3d')
#~ ax.fill(lons,lats,eles,'r')
#~ plt.show()
#~ exit(0)
xs = lons
ys = lats
zs = eles
ls = dists
### 3D plot
# Code to convert data in 3D polygons
v = []
h = min(zs)
for k in range(0, len(xs) - 1):
x = [xs[k], xs[k + 1], xs[k + 1], xs[k]]
y = [ys[k], ys[k + 1], ys[k + 1], ys[k]]
z = [zs[k], zs[k + 1], h, h]
v.append(zip(x, y, z))
poly3dCollection = Poly3DCollection(v,
facecolors=(0.4, 0.4, 0.4, 0.5),
edgecolors='none')
dpi = 100
width = 200
height = 150
# Code to plot the 3D polygons
plt.rcParams['axes.labelsize'] = 1
fig = plt.figure(figsize=(width / dpi, height / dpi), dpi=dpi)
#~ ax = Axes3D(fig)
ax = fig.gca(projection='3d')
ax.add_collection3d(poly3dCollection)
ax.set_xlim([min(xs), max(xs)])
ax.set_ylim([min(ys), max(ys)])
ax.set_zlim([min(zs), max(zs)])
#~ ax.set_axis_off()
# Get rid of the spines
#~ ax.w_xaxis.line.set_color((1.0, 1.0, 1.0, 0.0))
#~ ax.w_yaxis.line.set_color((1.0, 1.0, 1.0, 0.0))
# Get rid of the ticks
ax.zaxis._axinfo['tick']['inward_factor'] = 0
ax.zaxis._axinfo['tick']['outward_factor'] = 0.2
ax.set_xticks([])
ax.set_yticks([])
ax.set_zticks([int(min(zs)), int(max(zs))])
ax.set_zticks([])
zed = [tick.label.set_fontsize(7) for tick in ax.zaxis.get_major_ticks()]
plt.tight_layout(pad=0.1)
fig.savefig(profile_filename + '-3d.png', dpi=dpi)
#plt.show()
### Way plot
fig, ax = plt.subplots()
fig.set_size_inches(width / dpi, height / dpi, forward=True)
fig.set_dpi(dpi)
ax.set_xticks([])
ax.set_yticks([])
plt.axis('off')
ax.plot(xs, ys, alpha=0.6, linewidth=3, color='r')
ax.set_xlim([
min(xs) - (max(xs) - min(xs)) / 10,
max(xs) + (max(xs) - min(xs)) / 10
])
ax.set_ylim([
min(ys) - (max(ys) - min(ys)) / 10,
max(ys) + (max(ys) - min(ys)) / 10
])
l = sqrt((max(xs) - min(xs))**2 + ((max(ys) - min(ys))**2)) / 10
a = math.atan(1 / (xs[1] - xs[0]) * (ys[1] - ys[0]))
y2 = ys[0] + math.sin(a) * l
x2 = xs[0] + math.cos(a) * l
arrow = dict(facecolor=(0.1, 0.1, 0.1),
edgecolor=(0.1, 0.1, 0.1),
headwidth=6,
frac=0.3,
width=2)
plt.annotate(s='', xy=(x2, y2), xytext=(xs[0], ys[0]), arrowprops=arrow)
plt.tight_layout(pad=0.1)
fig.savefig(profile_filename + '-2d.png', dpi=dpi)
#~ plt.show()
### profileplot
fig, ax = plt.subplots()
fig.set_size_inches(width / dpi, height / dpi, forward=True)
fig.set_dpi(dpi)
ax.set_xticks([])
#~ ax.set_yticks([])
#~ plt.axis('off')
ax.spines['bottom'].set_color((1.0, 1.0, 1.0, 0.5))
ax.spines['top'].set_color((1.0, 1.0, 1.0, 0))
ax.spines['left'].set_color((1.0, 1.0, 1.0, 0))
ax.spines['right'].set_color((1.0, 1.0, 1.0, 0))
ax.tick_params(axis='y', colors=(0, 0, 0, 0.7))
ax.plot(ls, zs, alpha=0.6, linewidth=1, color=(0.5, 0.5, 0.5))
ax.fill_between(ls,
min(zs),
zs,
facecolor=(0, 0, 0, 0.3),
interpolate=True)
ax.set_yticks([int(min(zs)), int(max(zs))])
zed = [tick.label.set_fontsize(7) for tick in ax.yaxis.get_major_ticks()]
plt.tight_layout(pad=0.1)
fig.savefig(profile_filename + '-ele.png', dpi=dpi)
return profile_filename
def show_3d_survey_geometry(self, elev, azim, show_block=False):
X1, X2 = -250.0, 250.0
Y1, Y2 = -250.0, 250.0
Z1, Z2 = -400.0, 0.0
def polyplane(verts, alpha=0.1, color="green"):
poly = Poly3DCollection(verts)
poly.set_alpha(alpha)
poly.set_facecolor(color)
return poly
z1 = -100.0
x = np.r_[X1, X2, X2, X1, X1]
y = np.ones(5) * 0.0
z = np.r_[Z1, Z1, Z2, Z2, Z1]
verts = [list(zip(x, y, z))]
polyplane(verts, color="green")
x = np.r_[X1, X2, X2, X1, X1]
y = np.r_[Y1, Y1, Y2, Y2, Y1]
z = np.ones(5) * 0.0
verts = [list(zip(x, y, z))]
polyplane(verts, color="grey")
x = np.r_[X1, X2, X2, X1, X1]
y = np.r_[Y1, Y1, Y2, Y2, Y1]
z = np.ones(5) * z1
verts = [list(zip(x, y, z))]
polyplane(verts, color="grey")
fig = plt.figure(figsize=(8, 8))
ax = fig.gca(projection="3d")
ax.plot3D(np.r_[-200, 200], np.r_[0, 0], np.r_[1, 1] * 0.0, "r-", lw=3)
ax.plot3D(
self.mesh.gridCC[:, 0],
self.mesh.gridCC[:, 1],
np.zeros_like(self.mesh.gridCC[:, 0]),
"k.",
)
ax.legend(("Tx", "Rx"), loc=1)
if show_block:
xc, yc, zc = 0, 0, 0
x1, x2 = -40, 40
y1, y2 = -40, 40
z1, z2 = -160, -80
x = np.r_[x1, x2, x2, x1, x1]
y = np.ones(5) * 0.0
z = np.r_[z1, z1, z2, z2, z1]
ax.plot3D(x, y, z, "k--")
x = np.r_[x1, x2, x2, x1, x1]
y = np.r_[y1, y1, y2, y2, y1]
z = np.ones(5) * (z1 + z2) / 2.0
ax.plot3D(x, y, z, "k--")
block_xyz = np.asarray([
[x1, x1, x2, x2, x1, x1, x2, x2],
[y1, y2, y2, y1, y1, y2, y2, y1],
[z1, z1, z1, z1, z2, z2, z2, z2],
])
xyz = block_xyz.T
# Face 1
ax.add_collection3d(
Poly3DCollection(
[
list(
zip(xyz[:4, 0] + xc, xyz[:4, 1] + yc,
xyz[:4, 2] + zc))
],
facecolors="k",
alpha=0.5,
))
# Face 2
ax.add_collection3d(
Poly3DCollection(
[
list(
zip(xyz[4:, 0] + xc, xyz[4:, 1] + yc,
xyz[4:, 2] + zc))
],
facecolors="k",
alpha=0.5,
))
# Face 3
ax.add_collection3d(
Poly3DCollection(
[
list(
zip(
xyz[[0, 1, 5, 4], 0] + xc,
xyz[[0, 1, 5, 4], 1] + yc,
xyz[[0, 1, 5, 4], 2] + zc,
))
],
facecolors="k",
alpha=0.5,
))
# Face 4
ax.add_collection3d(
Poly3DCollection(
[
list(
zip(
xyz[[3, 2, 6, 7], 0] + xc,
xyz[[3, 2, 6, 7], 1] + yc,
xyz[[3, 2, 6, 7], 2] + zc,
))
],
facecolors="k",
alpha=0.5,
))
# Face 5
ax.add_collection3d(
Poly3DCollection(
[
list(
zip(
xyz[[0, 4, 7, 3], 0] + xc,
xyz[[0, 4, 7, 3], 1] + yc,
xyz[[0, 4, 7, 3], 2] + zc,
))
],
facecolors="k",
alpha=0.5,
))
# Face 6
ax.add_collection3d(
Poly3DCollection(
[
list(
zip(
xyz[[1, 5, 6, 2], 0] + xc,
xyz[[1, 5, 6, 2], 1] + yc,
xyz[[1, 5, 6, 2], 2] + zc,
))
],
facecolors="k",
alpha=0.5,
))
ax.set_xlim(X1, X2)
ax.set_ylim(Y1, Y2)
ax.set_zlim(Z1, Z2)
ax.set_xlabel("X (m)")
ax.set_ylabel("Y (m)")
ax.set_zlabel("Depth (m)")
# ax.set_aspect("equal")
ax.view_init(elev=elev, azim=azim)
plt.show()
# list of faces
faces = [[Z[0], Z[1], Z[2], Z[3]], [Z[4], Z[5], Z[6], Z[7]],
[Z[0], Z[1], Z[5], Z[4]], [Z[2], Z[3], Z[7], Z[6]],
[Z[1], Z[2], Z[6], Z[5]], [Z[4], Z[7], Z[3], Z[0]]]
# Plot the cube in 3D
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.add_collection3d(
Poly3DCollection(faces,
facecolors='cyan',
linewidths=1,
edgecolors='r',
alpha=.75))
ax.scatter(Z[:, 0], Z[:, 1], Z[:, 2])
ax.set_xlim(0, 11), ax.set_ylim(0, 11), ax.set_zlim(0, 11)
ax.set_aspect('equal') # uniform scale axes
#Use the same method from before to project the 3D points to 2D
pts2d = None
# TODO: your code here
K = np.array([[800, 0, 320], [0, 800, 240], [0, 0, 1]], dtype=np.float32)
pts2d = cv2.projectPoints(np.float32(Z),
rvec=(0, 0, 0),
tvec=(0, 0, 0),
cameraMatrix=K,
distCoeffs=None)[0]
def ShowDeformation(t=0):
I = np.eye(3)
F = I + (DeformationGradient - I) * t
Y1 = F.dot(X1)
Y2 = F.dot(X2)
Y3 = F.dot(X3)
Y4 = F.dot(X4)
P1 = np.array([X1[0][0], X1[1][0], X1[2][0]])
P2 = np.array([X2[0][0], X2[1][0], X2[2][0]])
P3 = np.array([X3[0][0], X3[1][0], X3[2][0]])
P4 = np.array([X4[0][0], X4[1][0], X4[2][0]])
# vertices of a pyramid
Vertices = np.array([P1, P2, P3, P4])
Center1 = Vertices.sum(axis=0) / 4
Vectors1 = Vertices - Center1
plt.cla()
Axis.scatter3D(Vertices[:, 0],
Vertices[:, 1],
Vertices[:, 2],
facecolor="blue")
# generate list of sides' polygons of our pyramid
Faces = [[Vertices[0], Vertices[1], Vertices[2]],
[Vertices[0], Vertices[1], Vertices[3]],
[Vertices[0], Vertices[2], Vertices[3]],
[Vertices[1], Vertices[2], Vertices[3]]]
# plot sides
Axis.add_collection3d(
Poly3DCollection(Faces,
facecolors='blue',
linewidths=1,
edgecolors='blue',
alpha=.25))
P1 = np.array([Y1[0][0], Y1[1][0], Y1[2][0]])
P2 = np.array([Y2[0][0], Y2[1][0], Y2[2][0]])
P3 = np.array([Y3[0][0], Y3[1][0], Y3[2][0]])
P4 = np.array([Y4[0][0], Y4[1][0], Y4[2][0]])
# vertices of a pyramid
Vertices = np.array([P1, P2, P3, P4])
Center2 = Vertices.sum(axis=0) / 4
Vectors2 = Vertices - Center2
Axis.scatter3D(Vertices[:, 0],
Vertices[:, 1],
Vertices[:, 2],
facecolor="red")
# generate list of sides' polygons of our pyramid
Faces = [[Vertices[0], Vertices[1], Vertices[2]],
[Vertices[0], Vertices[1], Vertices[3]],
[Vertices[0], Vertices[2], Vertices[3]],
[Vertices[1], Vertices[2], Vertices[3]]]
# plot sides
Axis.add_collection3d(
Poly3DCollection(Faces,
facecolors='red',
linewidths=1,
edgecolors='red',
alpha=.25))
# add displacement arrows
Axis.quiver(X1[0][0],
X1[1][0],
X1[2][0],
Y1[0][0] - X1[0][0],
Y1[1][0] - X1[1][0],
Y1[2][0] - X1[2][0],
color=(0, 0, 0),
linewidth=2)
Axis.quiver(X2[0][0],
X2[1][0],
X2[2][0],
Y2[0][0] - X2[0][0],
Y2[1][0] - X2[1][0],
Y2[2][0] - X2[2][0],
color=(0, 0, 0),
linewidth=2)
Axis.quiver(X3[0][0],
X3[1][0],
X3[2][0],
Y3[0][0] - X3[0][0],
Y3[1][0] - X3[1][0],
Y3[2][0] - X3[2][0],
color=(0, 0, 0),
linewidth=2)
Axis.quiver(X4[0][0],
X4[1][0],
X4[2][0],
Y4[0][0] - X4[0][0],
Y4[1][0] - X4[1][0],
Y4[2][0] - X4[2][0],
color=(0, 0, 0),
linewidth=2)
# make the panes transparent
Axis.xaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))
Axis.yaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))
Axis.zaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))
# make the grid lines transparent
Axis.xaxis._axinfo["grid"]['color'] = (1, 1, 1, 0)
Axis.yaxis._axinfo["grid"]['color'] = (1, 1, 1, 0)
Axis.zaxis._axinfo["grid"]['color'] = (1, 1, 1, 0)
# modify ticks
# Axis.set_xticks([-1, 0, 1])
# Axis.set_yticks([-1, 0, 1])
# Axis.set_zticks([-1, 0, 1])
# set limits
Center = (Center1 + Center2) / 2
Vertices1 = Vectors1 + Center1
Vertices2 = Vectors2 + Center2
Vectors1 = Vertices1 - Center
Vectors2 = Vertices2 - Center
Max = max(np.abs(Vectors1).max(), np.abs(Vectors2).max())
Axis.set_xlim(Center[0] - Max, Center[0] + Max)
Axis.set_ylim(Center[1] - Max, Center[1] + Max)
Axis.set_zlim(Center[2] - Max, Center[2] + Max)
# set axes labels
Axis.xaxis.set_rotate_label(False) # disable automatic rotation
Axis.yaxis.set_rotate_label(False) # disable automatic rotation
Axis.zaxis.set_rotate_label(False) # disable automatic rotation
Axis.set_xlabel('e$_1$', rotation=0)
Axis.set_ylabel('e$_2$', rotation=0)
Axis.set_zlabel('e$_3$', rotation=0)
plt.show()
return
l_plane = 1.5
c1 = normal + l_plane * default_x_axis + l_plane * default_y_axis
c2 = normal + l_plane * default_x_axis - l_plane * default_y_axis
c3 = normal - l_plane * default_x_axis - l_plane * default_y_axis
c4 = normal - l_plane * default_x_axis + l_plane * default_y_axis
x = np.array([c1[0], c2[0], c3[0], c4[0]])
y = np.array([c1[1], c2[1], c3[1], c4[1]])
z = np.array([c1[2], c2[2], c3[2], c4[2]])
verts = [list(zip(x, y, z))]
# xx, yy = np.meshgrid(xx, yy)
pc = Poly3DCollection(verts, facecolors='C0', alpha=0.5, linewidths=1)
pc.set_alpha(0.5)
pc.set_facecolor('C0')
ax.add_collection3d(pc)
palette = sns.color_palette()
# plot the axes lines
l = 3
ax.plot([0, l], [0, 0], [0, 0], color=palette[0], linewidth=3)
ax.plot([0, 0], [0, l], [0, 0], color=palette[1], linewidth=3)
ax.plot([0, 0], [0, 0], [0, l], color=palette[2], linewidth=3)
ax.plot([-l, 0], [0, 0], [0, 0], color=palette[0], linestyle=':', linewidth=3)
ax.plot([0, 0], [-l, 0], [0, 0], color=palette[1], linestyle=':', linewidth=3)
ax.plot([0, 0], [0, 0], [-l, 0], color=palette[2], linestyle=':', linewidth=3)
from mpl_toolkits.mplot3d import Axes3D from mpl_toolkits.mplot3d.art3d import Poly3DCollection import matplotlib.pyplot as plt fig = plt.figure() ax = Axes3D(fig) x = [0,1,1,0] y = [0,0,1,1] z = [0,1,0,1] verts = [zip(x, y,z)] ax.add_collection3d(Poly3DCollection(verts)) plt.show()
def PlotCell(self, d1, d2, d3, d4, d5, d6, dat, faces, l1, l2, l3, l4, l5, l6, l7, l8, labels, n1, n2, n3, n4, n5, n6, xyz, show=False):
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d import proj3d
from matplotlib.lines import Line2D
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
import matplotlib.pyplot as plt
fig = plt.figure(figsize=(10, 10), dpi=90)
ax = fig.add_subplot(111, projection='3d')
ax.plot([l1[0], l4[0]], [l1[1], l4[1]], [l1[2], l4[2]], 'k-')
ax.plot([l4[0], l3[0]], [l4[1], l3[1]], [l4[2], l3[2]], 'k*-.')
ax.plot([l3[0], l2[0]], [l3[1], l2[1]], [l3[2], l2[2]], 'k-')
ax.plot([l2[0], l1[0]], [l2[1], l1[1]], [l2[2], l1[2]], 'k*-.')
ax.plot([l5[0], l8[0]], [l5[1], l8[1]], [l5[2], l8[2]], 'k-')
ax.plot([l8[0], l7[0]], [l8[1], l7[1]], [l8[2], l7[2]], 'k*-.')
ax.plot([l7[0], l6[0]], [l7[1], l6[1]], [l7[2], l6[2]], 'k-')
ax.plot([l6[0], l5[0]], [l6[1], l5[1]], [l6[2], l5[2]], 'k*-.')
ax.plot([l1[0], l5[0]], [l1[1], l5[1]], [l1[2], l5[2]], 'k-')
ax.plot([l2[0], l6[0]], [l2[1], l6[1]], [l2[2], l6[2]], 'k--')
ax.plot([l4[0], l8[0]], [l4[1], l8[1]], [l4[2], l8[2]], 'k-')
ax.plot([l3[0], l7[0]], [l3[1], l7[1]], [l3[2], l7[2]], 'k-')
ax.scatter(l1[0], l1[1], l1[2], c='r', s=25)
ax.scatter(l2[0], l2[1], l2[2], c='g', s=25)
ax.scatter(l3[0], l3[1], l3[2], c='y')
ax.scatter(l4[0], l4[1], l4[2], c='b')
ax.scatter(l5[0], l5[1], l5[2], c='k')
ax.scatter(l6[0], l6[1], l6[2], c='k')
ax.scatter(l7[0], l7[1], l7[2], c='k')
ax.scatter(l8[0], l8[1], l8[2], c='k')
ax.scatter(xyz[0], xyz[1], xyz[2], c='y', s=25)
ax.set_xlabel("X-Axis")
ax.set_ylabel("Y-Axis")
ax.set_zlabel("Z-Axis")
# ==================================================
# Verification Plotting only between double lines.
ln1x = [l1[0], xyz[0]]
ln1y = [l1[1], xyz[1]]
ln1z = [l1[2], xyz[2]]
ax.plot(ln1x, ln1y, ln1z, 'k-')
ln7x = [l7[0], xyz[0]]
ln7y = [l7[1], xyz[1]]
ln7z = [l7[2], xyz[2]]
ax.plot(ln7x, ln7y, ln7z, 'b-')
# ===================================================
# =================================================================================
# Verification plotting ONLY between double lines
#
#
# print ("d1: {}".format(d1))
# print ("d2: {}".format(d2))
# print ("d3: {}".format(d3))
# print ("d4: {}".format(d4))
# print ("d5: {}".format(d5))
# print ("d6: {}".format(d6))
dn1 = n1 * d1
dn2 = n2 * d2
dn3 = n3 * d3
dn4 = n4 * d4
dn5 = n5 * d5
dn6 = n6 * d6
ax.scatter((xyz + dn1)[0], (xyz + dn1)[1], (xyz + dn1)[2], c='r', marker='*')
ax.scatter((xyz + dn2)[0], (xyz + dn2)[1], (xyz + dn2)[2], c='r', marker=">")
ax.scatter((xyz + dn3)[0], (xyz + dn3)[1], (xyz + dn3)[2], c='b', marker="*")
ax.scatter((xyz + dn4)[0], (xyz + dn4)[1], (xyz + dn4)[2], c='b', marker="<")
ax.scatter((xyz + dn5)[0], (xyz + dn5)[1], (xyz + dn5)[2], c='r', marker="^")
ax.scatter((xyz + dn6)[0], (xyz + dn6)[1], (xyz + dn6)[2], c='b', marker="v")
# print ("V1: {}".format(v1))
# print ("V2: {}".format(v2))
fcolors = ['r', 'g', 'b', 'y', 'k', 'w']
count = 0
face_plots = []
face_legends = []
for face in faces:
x, y, z = np.hsplit(face, 3)
x = x.flatten()
y = y.flatten()
z = z.flatten()
verts = [zip(x, y, z)]
ax.add_collection3d(Poly3DCollection(verts, alpha=0.5, color=fcolors[count]))
face_plots.append(Line2D([0], [0], linestyle="none", marker="s", alpha=0.5, markersize=10, markerfacecolor=fcolors[count]))
face_legends.append("Face {}".format(count + 1))
count += 1
ax.legend(face_plots, face_legends, numpoints=1, loc='best')
# print("Requested Point: {}".format(xyz))
# print("Labels: {}".format(labels))
# print("Locations: {}".format(dat))
# print("Length of Labels: {}".format(len(labels)))
for a in range(len(labels)):
x, y, z = dat[a]
lab = ax.text(x, y, z, " p{}".format(str(a + 1)), size=10, zorder=1, color='r')
# plt.figtext(0.02, 0.01, "Face Distances from point {}:\n1: {}\n2: {}\n3: {}\n4: {}\n5: {}\n6: {}".format(xyz, d1, d2, d3, d4, d5, d6), size=10, zorder=1, color='k')
# =================================================================================
fig.savefig("points/point_{}.pdf".format(xyz))
if show:
plt.show()
plt.close(fig)
