def Nneighbours(node, NC, Tri, layer):
# determine neighbouring nodes of a specific node up to a set of "layers"
# inputs:
# node: specific node to query neighbours, NC&Tri: nodal coord and connectivity
# layer: up to how many degrees of separation a neighbour shoud be searched
aa = np.where(Tri == node)[0]
pn = Tri[aa, ].reshape((aa.size * 3, ))
neigh = find_repeats(pn)[0]
if layer > 1:
for l in range(1, layer):
for nn in neigh:
aa = np.where(Tri == nn)[0]
pn = Tri[aa, ].reshape((aa.size * 3, ))
pn = find_repeats(pn)[0]
for i in pn:
if find_repeats(np.r_[neigh, i])[0].size == 0:
neigh = np.r_[neigh, i]
neigh = np.array(neigh[np.where(neigh <> node)[0], ], int)
#if layer==1: #if only actual neighbours are calculated, returmn then in right hand rule order for retriangulation purposes
#neighC=np.empty((neigh.size,))
#neighC[0,]=neigh[0,]
#rp,cp=np.where(Tri[neighpos,]==neigh[0,])
#for i in range(1,neigh.size):
#r,c=np.where((Tri[neighpos[rp,]]<>neighC[i-1,])&(Tri[neighpos[rp,]]<>node))
#neighC[i,]=max(((cp+1==c)|((cp==2)*(c==0)))*Tri[neighpos[rp,],c])
#rp,cp=np.where(Tri[neighpos,]==neighC[i,])
#neigh = np.array(neighC,int)
return neigh
def AllowableNaT(NC,
Tconnect,
FeatAreaNodes,
AllowNodes,
Rlines,
Vlines,
keepLNnodes,
doTri=1):
AllowTri = []
RemoveNodes = np.array([])
LineNodes = np.array([])
print "Get line nodes and set up kd-tree"
for i in range(1, Rlines[0] + 1):
LineNodes = np.array(np.r_[LineNodes, Rlines[i]], int)
for i in range(1, Vlines[0] + 1):
LineNodes = np.array(np.r_[LineNodes, Vlines[i]], int)
kdtLN = KDTree(NC[LineNodes, ], 5)
print "Find allowable and remove additional nodes"
for i in FeatAreaNodes:
cn = LineNodes[np.array(kdtLN.query(NC[i, ])[1], int)]
if np.where(keepLNnodes == cn)[0].size > 0:
AllowNodes = np.r_[AllowNodes, i]
else:
RemoveNodes = np.r_[RemoveNodes, i]
AllowNodes, RemoveNodes = np.array(AllowNodes,
int), np.array(RemoveNodes, int)
# remove possible repeated indices from "AllowNodes"
#remove=find_repeats(AllowNodes)[0]
if doTri == 1:
print "Update allowable triangles"
for i in range(Tconnect.shape[0]):
if find_repeats(np.r_[AllowNodes, Tconnect[i, ]])[0].size > 0:
AllowTri.append(i)
AllowTri = np.array(AllowTri, int)
return AllowNodes, RemoveNodes, AllowTri
def _rank1d(data, keep_na="False"):
"""
From numpy.stats.mstats.
Difference: Tie breaking is randomly resolved.
Arguments:
data {[type]} -- [description]
Raises:
ValueError -- [description]
NotImplementedError -- [description]
Returns:
[type] -- [description]
"""
data = np.ma.array(data, copy=False)
n = data.count()
rk = np.empty(data.size, dtype=float)
idx = data.argsort()
rk[idx[:n]] = np.arange(1, n + 1)
repeats = mstats.find_repeats(data.copy())
for r in repeats[0]:
condition = (data == r).filled(False)
rk[condition] = np.random.permutation(rk[condition])
# keep nas
if (keep_na):
rk[np.isnan(data)] = np.nan
return rk
def NodeselectFP(NC,Tri,Neig,vv):
#spheres&saddles:
spsad=np.where((Neig[:,0]<1.5*Neig[:,1])&(Neig[:,1]<1.5*Neig[:,2])&(Neig[:,2]>0))[0]
rest=np.where((Neig[:,0]>=1.5*Neig[:,1])|(Neig[:,1]>=1.5*Neig[:,2])|(Neig[:,2]<=0))[0]
print "Nr of Spheres & Sadles: ",spsad.size
#ridges and valleys
ridgeval1=np.where((Neig[rest,0]<1.5*Neig[rest,1])&(Neig[rest,1]>10*Neig[rest,2])&(np.abs(Neig[rest,2])<0.001))[0]
ridgeval=rest[ridgeval1,]
rest1=np.where((Neig[rest,0]>=1.5*Neig[rest,1])|(Neig[rest,1]<=10*Neig[rest,2])|(np.abs(Neig[rest,2])>=0.001))[0]
rest=rest[rest1,]
print "Nr of Ridges & Valleys: ",ridgeval.size
#planes:
plane1=np.where((Neig[rest,0]>10*Neig[rest,1])&(np.abs(Neig[rest,1])<0.001)&(np.abs(Neig[rest,2])<0.001))[0]
plane=rest[plane1,]
rest1=np.where((Neig[rest,0]<=10*Neig[rest,1])|(np.abs(Neig[rest,1])>=0.001)|(np.abs(Neig[rest,2])>=0.001))[0]
rest=rest[rest1,]
print "Nr of Planes: ",plane.size
#keep all for eig1 < 3*eig2
keep1=np.where(Neig[rest,0]<5*Neig[rest,1])[0]
keep = np.r_[spsad,ridgeval,keep1] # take all features&sharp edges except planes
rest=np.where(Neig[rest,0]>=5*Neig[rest,1])[0]
track=0
##keep every 2nd for eig1<20*eig2 and every 3rd for eig<500*eig2:
#Neig=np.ma.load('EigvalDolph1n.txt')
##vv=np.array([50,100,1000])
for inc in vv:
track=track+1
print "Step ",track," of ",vv.size
rows2=np.where(Neig[rest,0]<inc*Neig[rest,1])[0]
rest1=np.where(Neig[rest,0]>=inc*Neig[rest,1])[0]
rows2=rest[rows2,]
rest=rest[rest1,]
if rows2.size > 0:
cont=1
while cont>0:
node = rows2[0,]
keep=np.r_[keep,node]
neigh=Nneighbours(node,NC,Tri,track)[1]
torem=find_repeats(np.r_[rows2,neigh])[0]
for i in np.r_[node,torem]:
rows2 = rows2[np.r_[np.where(rows2<i)[0],np.where(rows2>i)[0]],]
#print 'possible selections in current category: ',rows2.size
if rows2.size==0:
cont=0
#for i in rows2:
#print "node: ",i
#neigh=Nneighbours(i,NC,Tri,track)
#if find_repeats(np.r_[keep,neigh])[0].size==0:
#keep=np.r_[keep,i]
#print " keep"
keep=np.array(keep,int)
keep.sort()
return keep
def NodeselectFP(NC, Tri, layer):
Neig = Neigenvalues(NC, Tri, layer)
#spheres&saddles:
spsad = np.where((Neig[:, 0] < 1.5 * Neig[:, 1])
& (Neig[:, 1] < 1.5 * Neig[:, 2]) & (Neig[:, 2] > 0))[0]
rest = np.where((Neig[:, 0] >= 1.5 * Neig[:, 1])
| (Neig[:, 1] >= 1.5 * Neig[:, 2]) | (Neig[:, 2] <= 0))[0]
print "Nr of Spheres & Sadles: ", spsad.size
#ridges and valleys
ridgeval1 = np.where((Neig[rest, 0] < 1.5 * Neig[rest, 1])
& (Neig[rest, 1] > 10 * Neig[rest, 2])
& (np.abs(Neig[rest, 2]) < 0.001))[0]
ridgeval = rest[ridgeval1, ]
rest1 = np.where((Neig[rest, 0] >= 1.5 * Neig[rest, 1])
| (Neig[rest, 1] <= 10 * Neig[rest, 2])
| (np.abs(Neig[rest, 2]) >= 0.001))[0]
rest = rest[rest1, ]
print "Nr of Ridges & Valleys: ", ridgeval.size
#planes:
plane1 = np.where((Neig[rest, 0] > 10 * Neig[rest, 1])
& (np.abs(Neig[rest, 1]) < 0.001)
& (np.abs(Neig[rest, 2]) < 0.001))[0]
plane = rest[plane1, ]
rest1 = np.where((Neig[rest, 0] <= 10 * Neig[rest, 1])
| (np.abs(Neig[rest, 1]) >= 0.001)
| (np.abs(Neig[rest, 2]) >= 0.001))[0]
rest = rest[rest1, ]
print "Nr of Planes: ", planes.size
#keep all for eig1 < 3*eig2
keep1 = np.where(Neig[rest, 0] < 3 * Neig[rest, 1])[0]
keep = np.r_[spsad, ridgeval,
keep1] # take all features&sharp edges except planes
rest = np.where(Neig[rest, 0] >= 3 * Neig[rest, 1])[0]
track = 0
##keep every 2nd for eig1<20*eig2 and every 3rd for eig<500*eig2:
#Neig=np.ma.load('EigvalDolph1n.txt')
vv = np.array([20, 500])
for inc in vv:
track = track + 1
print "Step ", track, " of ", vv.size
rows2 = np.where(Neig[rest, 0] < inc * Neig[rest, 1])[0]
rest1 = np.where(Neig[rest, 0] >= inc * Neig[rest, 1])[0]
rows2 = rest[rows2, ]
rest = rest[rest1, ]
for i in rows2:
print "node: ", i
neigh = Nneighbours(i, NC, Tri, track)
if find_repeats(np.r_[keep, neigh])[0].size == 0:
keep = np.r_[keep, i]
print " keep"
keep = np.array(keep, int)
keep.sort()
return keep
def TriEdge(node,NC,Tri):
# determine edge returned as neighbouring node and triangles on either side of edges
triangles = []
aa=np.where(Tri==node)[0]
pn=Tri[aa,].reshape((aa.size*3,))
neigh=find_repeats(pn)[0]
neighOne = np.array(neigh,int)
neighOne = neighOne[np.where(neighOne<>node)[0]]
for i in neighOne:
tr = np.where(Tri[aa,]==i)[0]
triangles = triangles+[[aa[tr[0]],aa[tr[1]]]]
triangles = np.array(triangles,int)
return neighOne,triangles
def EQweight(NCinner, NC, inner, Tet, EQprev, deltPrescr):
EQ = np.r_[EQprev]
NCcur = np.r_[NC]
NCDIFF = NCinner.reshape((inner.size, 3)) - NC[inner, ]
NCcur[inner, ] = NCinner.reshape((inner.size, 3))
nodes = inner[np.where(np.sum(NCDIFF * NCDIFF, 1) > 0)[0]]
tets = np.array([])
if nodes.size > 0:
for i in nodes:
tets = np.r_[tets, np.where(Tet == i)[0]]
#tets = np.array(tets,int)
tets = np.array(find_repeats(np.r_[tets, tets])[0], int)
if tets.size > 0:
EQ[tets] = elemQual_mu(tets, NCcur, Tet, 0, deltPrescr)[0]
COST = np.sum(1 / EQ)
return COST
def elasticsurf(NCB,
ConnectB,
LandmB,
LandmB_NC,
AllowableBI,
NCT,
ConnectT,
AllowableT,
UseN_B,
UseN_T,
k_max,
USENORMALS,
gamm=2,
sigm0=10,
f=1.0715):
# Elastic surface registration:
#inputs:
# NCB,NCT: nodal coordinates of base and target surfaces
# ConnectB;ConnectT: Base&target connectivity
# LandmB,LandmB_NC landmarks that have to have a 1 to 1 correspondence (input 0 no landmarks are present)
# UseN_B & AllowableB: Feature dependant nodes on Base-mesh (indices in NCB) and allowable triangles to match.
# UseN_T & AllowableT: Selective Feature preserving nodes and triangles (indices in NCT and ConnectT) on target mesh.
# k_max: maximum number of iterations
######## ADDITIONAL SETTINGS REQUIRED ARE SET INTERNAL TO CODE #########
print
print "SELECTIVE MESH MORPHING ALGORITHM USING ELASTIC SURFACE REGISTRATION"
print " -G.J.J.v.Rensburg - 22/04/2010-"
t_start = time.clock()
ConnectB = np.array(ConnectB, int)
ConnectT = np.array(ConnectT, int)
#LandmB = np.array(LandmB[:,0],int) # do -1 later to be consistent with python indexing, first need to do other "temporary landmarks"& check that they dont fall on actual landmark positions!
# Settings for elastic surface registration:
m = 20 # nearest neighbour parameter
alph = 0.5 # normilization factor
#gamm=2 # smoothing parameter1
#sigm0=10 # smoothing parameter2
#f=1.0715 # smoothing parameter3
Tol = 0.0001 # stopping criteria
# determine N1,N2,T1 and T2:
N1 = NCB.shape[0]
N2 = NCT.shape[0]
T1 = ConnectB.shape[0]
T2 = ConnectT.shape[0]
NL = LandmB.shape[0]
# For parallel programming devide Nr of computations by number of parallel processes (LIM)
NPP1 = N1 / LIM
NPP2 = N2 / LIM
################################ INITIALIZE & NODES OF CONCERN: #################################
########################################################################################################
print
print
print "Set up 1-ring neighbor list for all points on the generic mesh"
#neighbList = [[0]]*N1
#results = pprocess.Map(limit=LIM)
#calc = results.manage(pprocess.MakeParallel(Get1neigh))
#for j in range(0,LIM):
#calc(np.array(range(0,NPP1))+j*NPP1,NCB,ConnectB)
#for j in range(0,LIM):
#neighbList[j*NPP1:(1+j)*NPP1] = results[j]
#neighbList[LIM*NPP1:N1]=Get1neigh(np.array(range(LIM*NPP1,N1)),NCB,ConnectB)
#np.ma.dump(neighbList,'SkullSurf_neighbList')
neighbList = np.ma.load('SkullSurf_neighbList')
print
print "INITIALIZE SURFACE DEFORMATION"
CONV = []
print " enquire nodes where required displacement is checked"
###remove Landmarks from FDNB and SFPNT:
#for i in range(0,NL):
#if find_repeats(np.r_[UseN_B,LandmB[i,]])[0].size>0:
#r=np.where(UseN_B==LandmB[i,])[0]
#UseN_B = np.r_[UseN_B[0:r,],UseN_B[r+1:UseN_B.size,]]
SamplingB = UseN_B.size
SamplingT = UseN_T.size
## Full list of nodes used in Surface registration:
LMB = np.r_[
UseN_B] #,LandmB] # Last NL entries are reserved for Landmarks that HAVE TO FIT points on the target mesh
LMT = np.r_[UseN_T]
# For parallel programming devide Nr of computations by number of parallel processes (LIM)
SBPP = SamplingB / LIM
STPP = SamplingT / LIM
FMorph = 0
print
print "COARSE SURFACE REGISTRATION"
#print " Compute known displacement for Base_Landmarks "
#knownC = NCB[LandmB,]
#knownD = LandmB_NC-knownC
####print " using landmark displacements to deform using RBF"
####W_km1 = RBFmorph(NCB,knownC,knownD)
####tic = time.clock()
####W_km1 = MeshSmooth(W_km1,neighbList,10)
####print " Smoothing done in ",time.clock()-tic," seconds"
####np.ma.dump(W_km1,'TempElasNodes_Iter'+str(k-1)+'_Time'+time.ctime())
#print 'Smooth Gaussian Weight deformation to align Landmarks to target positions'
#k=0
#Err = 2
#W_km1 = np.r_[NCB]
#while (k<100)|(Err>Tol):
#k=k+1
#print 'Iteration : ',k
#DS = np.zeros((N1,3))
#knownC = W_km1[LandmB,]
#knownD = LandmB_NC-knownC
#knownD[np.isnan(knownD)]=0
## Deform mesh using Gaussian smoothing as suggested in paper by R.Bryan et al.
#sigma_k2 = np.power(np.power(f,-k)*20,2)
#results = pprocess.Map(limit=LIM)
#calc = results.manage(pprocess.MakeParallel(GaussianSmooth))
#for j in range(0,LIM):
#calc(np.array(range(0,NPP1))+j*NPP1,W_km1,knownC,knownD,sigma_k2,gamm)
#for j in range(0,LIM):
#DS[np.array(range(0,NPP1))+j*NPP1,:] = results[j]
#DS[range(LIM*NPP1,N1),:]=GaussianSmooth(np.array(range(LIM*NPP1,N1)),W_km1,knownC,knownD,sigma_k2,gamm)
#DS[np.isnan(DS)]=0
#W_km1 = W_km1+DS
#Err = np.sum(np.sqrt(np.sum(DS*DS,1)),0)/N1
#W_km1 = MeshSmooth(W_km1,neighbList,10)
#np.ma.dump(W_km1,'TempElasNodes_Iter0_TimeWedMar14_2011_20')
###np.ma.dump(W_km1,'TempElasNodes_Iter0_Time'+time.ctime())
W_km1 = NCB
################################ MAIN MESH DEFORMATION ALGORITHM: #################################
########################################################################################################
k = 1
print
print "ELASTIC SURFACE REGISTRATION"
print "determine vertex normals of target surface"
#Compute target-mesh triangle centroids:
print "determining centroids of target surface triangles"
S_2_centr = np.c_[np.sum(
np.c_[NCT[ConnectT[:, 0], 0], NCT[ConnectT[:, 1], 0],
NCT[ConnectT[:, 2], 0]], 1) / 3,
np.sum(
np.c_[NCT[ConnectT[:, 0], 1], NCT[ConnectT[:, 1], 1],
NCT[ConnectT[:, 2], 1]], 1) / 3,
np.sum(
np.c_[NCT[ConnectT[:, 0], 2], NCT[ConnectT[:, 1], 2],
NCT[ConnectT[:, 2], 2]], 1) / 3]
print "determine triangle and vertex normals of target surface"
TNORMT = np.cross(NCT[ConnectT[:, 1], :] - NCT[ConnectT[:, 0], :],
NCT[ConnectT[:, 2], :] - NCT[ConnectT[:, 0], :])
TNORMT = (TNORMT.T / (np.ones(
(3, 1)) * np.sqrt(np.sum(np.array([TNORMT * TNORMT]), 2)))).T
VNORMT = vrtxnormal(NCT, ConnectT, S_2_centr, TNORMT)
print "determining kd-trees of target surface centroids and nodal coordinates"
KDT_TC = KDTree(S_2_centr, m)
KDT_TN = KDTree(NCT, m)
print 'initialize absolute Gaussian weight for final displacement to preserve element quality'
GW = np.ones((SamplingB + SamplingT, 1))
while k <= k_max:
D1 = np.zeros((SamplingB, 3))
D2 = np.zeros((SamplingT, 3))
DS = np.zeros((N1, 3))
AllowableB = np.r_[AllowableBI]
print
print "MESH DEFORMATION ITERATION", k
print " determining known displacement of landmarks"
if NL > 0:
knownD = LandmB_NC - W_km1[LandmB, ]
print " determining centroids of deforming mesh"
W_km1_centr = np.c_[
np.sum(
np.c_[W_km1[ConnectB[:, 0], 0], W_km1[ConnectB[:, 1], 0],
W_km1[ConnectB[:, 2], 0]], 1) / 3,
np.sum(
np.c_[W_km1[ConnectB[:, 0], 1], W_km1[ConnectB[:, 1], 1],
W_km1[ConnectB[:, 2], 1]], 1) / 3,
np.sum(
np.c_[W_km1[ConnectB[:, 0], 2], W_km1[ConnectB[:, 1], 2],
W_km1[ConnectB[:, 2], 2]], 1) / 3]
print " determine triangle and vertex normals of deforming surface"
TNORMB = np.cross(W_km1[ConnectB[:, 1], :] - W_km1[ConnectB[:, 0], :],
W_km1[ConnectB[:, 2], :] - W_km1[ConnectB[:, 0], :])
TNORMB = (TNORMB.T / (np.ones(
(3, 1)) * np.sqrt(np.sum(np.array([TNORMB * TNORMB]), 2)))).T
VNORMB = vrtxnormal(W_km1, ConnectB, W_km1_centr, TNORMB)
print " determining kd-tree of current deforming surface centroids and nodal coordinates"
KDT_KC = KDTree(W_km1_centr, m)
KDT_KN = KDTree(W_km1, m)
#if find_repeats(np.r_[USENORMALS,k])[0].size>0:
#print " ### Use triangle and vertex normals in setting up point correspondence"
print " setting up D1(i,d)"
tic = time.clock()
results = pprocess.Map(limit=LIM)
calc = results.manage(pprocess.MakeParallel(DsetupNorm))
for j in range(0, LIM):
calc(
np.array(range(0, SBPP)) + j * SBPP, W_km1, VNORMB, NCT,
TNORMT, VNORMT, ConnectT, S_2_centr, AllowableT, LMB, D1)
for j in range(0, LIM):
D1[np.array(range(0, SBPP)) + j * SBPP, :] = results[j]
D1[range(LIM * SBPP, SamplingB), :] = DsetupNorm(
range(LIM * SBPP, SamplingB), W_km1, VNORMB, NCT, TNORMT, VNORMT,
ConnectT, S_2_centr, AllowableT, LMB, D1)
#D1=np.r_[D1,knownD]
print " ", time.clock() - tic, " seconds"
print " update allowable triangles on generic mesh:"
remP = D1[:, 0] + D1[:, 1] + D1[:, 2] == 0
removeP = LMB[remP]
print " unregistered points on generic mesh: ", removeP.size
print " number of original generic triangles allowed: ", AllowableB.shape[
0]
for rp in removeP:
rowsNo = np.where(AllowableB == rp)[0]
rowsNo.sort
for rr in rowsNo[::-1]:
AllowableB = AllowableB[np.where(
range(AllowableB.shape[0]) <> rr)[0], ]
print " number of generic triangles allowed for current iteration: ", AllowableB.shape[
0]
if find_repeats(np.r_[USENORMALS, k])[0].size > 0:
print " ### Use triangle and vertex normals in setting up point correspondence"
print " setting up D2(j,c)"
tic = time.clock()
results = pprocess.Map(limit=LIM)
calc = results.manage(pprocess.MakeParallel(DsetupNorm))
for j in range(0, LIM):
calc(
np.array(range(0, STPP)) + j * STPP, NCT, VNORMT, W_km1,
TNORMB, VNORMB, ConnectB, W_km1_centr, AllowableB, LMT, D2)
for j in range(0, LIM):
D2[np.array(range(0, STPP)) + j * STPP, :] = results[j]
D2[range(LIM * STPP, SamplingT), :] = DsetupNorm(
range(LIM * STPP, SamplingT), NCT, VNORMT, W_km1, TNORMB,
VNORMB, ConnectB, W_km1_centr, AllowableB, LMT, D2)
print " ", time.clock() - tic, " seconds"
else:
print " Simple closest point search iteration "
#print " setting up D1(i,d)"
#tic = time.clock()
#results = pprocess.Map(limit=LIM)
#calc = results.manage(pprocess.MakeParallel(Dsetup))
#for j in range(0,LIM):
#calc(np.array(range(0,SBPP))+j*SBPP,W_km1,NCT,ConnectT,S_2_centr,AllowableT,LMB,D1,KDT_TC,KDT_TN)
#for j in range(0,LIM):
#D1[np.array(range(0,SBPP))+j*SBPP,:] = results[j]
#D1[range(LIM*SBPP,SamplingB),:]=Dsetup(range(LIM*SBPP,SamplingB),W_km1,NCT,ConnectT,S_2_centr,AllowableT,LMB,D1,KDT_TC,KDT_TN)
##D1=np.r_[D1,knownD]
#print " ",time.clock()-tic," seconds"
#remP = D1[:,0]+D1[:,1]+D1[:,2]==0
#removeP = LMB[remP]
#print " unregistered points on generic mesh: ",removeP.size
#print " number of original generic triangles allowed: ",AllowableB.shape[0]
#for rp in removeP:
#rowsNo = np.where(AllowableB==rp)[0]
#rowsNo.sort
#for rr in rowsNo[::-1]:
#AllowableB = AllowableB[np.where(range(AllowableB.shape[0])<>rr)[0],]
#print " number of generic triangles allowed for current iteration: ",AllowableB.shape[0]
print " setting up D2(j,c)"
tic = time.clock()
results = pprocess.Map(limit=LIM)
calc = results.manage(pprocess.MakeParallel(Dsetup))
for j in range(0, LIM):
calc(
np.array(range(0, STPP)) + j * STPP, NCT, W_km1, ConnectB,
W_km1_centr, AllowableB, LMT, D2, KDT_KC, KDT_KN)
for j in range(0, LIM):
D2[np.array(range(0, STPP)) + j * STPP, :] = results[j]
D2[range(LIM * STPP, SamplingT), :] = Dsetup(
range(LIM * STPP, SamplingT), NCT, W_km1, ConnectB,
W_km1_centr, AllowableB, LMT, D2, KDT_KC, KDT_KN)
print " ", time.clock() - tic, " seconds"
# Compute displacement update for each node using suggested Gaussian radial basis function:
print " determining smoothed displacement field"
tic = time.clock()
NCp = np.r_[W_km1[LMB, :], NCT[LMT, :] + D2]
DD = np.r_[D1, -D2]
# Mask Nan and Inf values if any:
DD[np.isnan(DD)] = 0
DD[np.isinf(DD)] = 0
#keepP = DD[:,0]+DD[:,1]+DD[:,2]<>0
#print keepP
#NCp,DD = NCp[keepP,:],DD[keepP,:]
#KDTp = KDTree(NCp,5)
# Deform mesh using Gaussian smoothing as suggested in paper by R.Bryan et al.
sigma_k2 = np.power(np.power(f, -k) * sigm0, 2)
results = pprocess.Map(limit=LIM)
calc = results.manage(pprocess.MakeParallel(GaussianSmooth))
for j in range(0, LIM):
calc(
np.array(range(0, NPP1)) + j * NPP1, W_km1, NCp, DD, sigma_k2,
gamm)
for j in range(0, LIM):
DS[np.array(range(0, NPP1)) + j * NPP1, :] = results[j]
DS[range(LIM * NPP1, N1), :] = GaussianSmooth(
np.array(range(LIM * NPP1, N1)), W_km1, NCp, DD, sigma_k2, gamm)
print " ", time.clock() - tic, " seconds"
# Mask Nan and Inf if any:
DS[np.isnan(DS)] = 0
DS[np.isinf(DS)] = 0
#print 'Check if current iteration reduces element quality to below allowable and stiffen mesh accordingly'
print
print
print 'Convergence History'
print CONV
print
print
# Determine Jacobian of all elements and if unsattisfied apply stiffening (Decrease GW <1) untill this doesn't happen
# determine wheter convergence is acheived
#TotalMorph = np.sum(np.sqrt(np.sum(DS*DS,1)),0)/NCB.shape[0]
TotalMorph = np.sum(np.sqrt(np.sum(DD * DD, 1))) / (DD.size / 3)
CONV = CONV + [TotalMorph]
FMorph = (k == 1) * TotalMorph + FMorph
print " average nodal displacement for current deformation iteration:"
print TotalMorph
if (TotalMorph < Tol):
print
print "CONVERGED SOLUTION OBTAINED"
#CONV = CONV + [TotalMorph]
k = k_max * 10 + 1
W_km1 = W_km1 + DS
elif (k < 10) | (TotalMorph < 10 * FMorph):
print "problem not yet converged at iteration", k
#CONV = CONV + [TotalMorph]
k = k + 1
# Deform mesh:
print " deforming mesh (update of W_{k-1})"
W_km1 = W_km1 + DS
#np.ma.dump(W_km1,'Femur2NC_'+str(k))
else:
print "PROBLEM DIVERGING"
k = k_max * 10 - 1
#np.ma.dump(W_km1,'TempElasNodes_Iter'+str(k-1)+'_Time'+time.ctime())
if (k > 2) & (np.mod(k - 1, 5) == 0):
print
#np.ma.dump(W_km1,'TempElasNodes_Iter'+str(k-1)+'_Time'+time.ctime())
#W_km1 = RBFmorph(W_km1,W_km1[LandmB,],LandmB_NC-W_km1[LandmB,])
tic = time.clock()
W_km1 = MeshSmooth(W_km1, neighbList, 10)
np.ma.dump(
W_km1, 'SkullUnique2_gamm' + str(gamm) + '_sigN' + str(sigm0) +
'_iter' + str(k - 1))
print " Smoothing done in ", time.clock() - tic, " seconds"
#print "COARSE SURFACE REGISTRATION"
#print " using landmark displacements to deform using RBF"
#W_km1 = RBFmorph(W_km1,W_km1[LandmB,],LandmB_NC-W_km1[LandmB,])
print
if k == k_max + 1:
print
print "SOLUTION TERMINATED: maximum iterations,(", k_max, ") reached"
print
print "TOTAL TIME FOR ELASTIC SURFACE REGISTRATION : ", time.clock(
) - t_start, "seconds"
CONV = np.array(CONV)
return W_km1, CONV
for j in range(0, LIM):
DS[np.array(range(0, NPP1)) + j * NPP1, :] = results[j]
DS[range(LIM * NPP1, N1), :] = ptet.GaussianSmooth(
np.array(range(LIM * NPP1, N1)), np.r_[NCS], NCp, DD, sigma_k2, 2)
NCS[outer, ] = NCS[outer, ] + DispOuter
NCS[inner, ] = NCS[inner, ] + DS[inner, ]
EQ, delt, Sn2, Sig = qu.elemQual_mu(np.array(range(TetT.shape[0])), NCS,
TetT)
print ' Average Element Quality: ', np.average(EQ)
print ' Degenerate (q<0.15): ', np.where(EQ < 0.15)[0].size
print ' Inverted Elements: ', np.where(Sig < 0)[0].size
TetDeg = np.where(EQ < 0.15)[0]
DegNd = TetT[TetDeg, ]
DegNd = DegNd.reshape((DegNd.size, ))
DegRep = np.array(find_repeats(DegNd)[0], int)
for i in DegRep:
DegNd = DegNd[DegNd <> i]
DegNd = np.r_[DegNd, DegRep]
NCS[DegNd, ] = NCSprev[DegNd, ] + DS[DegNd, ]
#DegNd = np.array(find_repeats(np.r_[DegNd,outer])[0],int)
DegNd.sort()
PointConst = np.zeros((NCS.shape[0], ))
PointConst[outer, ] = 1
PointConst[DegNd, ] = 0
PointConst = np.array(PointConst, int)
print 'Construct VTK object for optimization'
##ADD CONTRAINTS AS POINT SCALARS
skvtk = pv.VtkData(pv.UnstructuredGrid(points=NCS, tetra=TetT),
'skull 4 symm',
def elasticsurf(NCB, ConnectB, LandmB, NCT, ConnectT, LandmT, FDNB, SFPNT,
SFPTT, k_max):
# Elastic surface registration:
#inputs:
# NCB,NCT: nodal coordinates of base and target surfaces
# ConnectB;ConnectT: Base&target connectivity
# LandmB,LandmT landmarks that have to have a 1 to 1 correspondence (input 0 no landmarks are present)
# FDN: Feature dependant nodes on Base-mesh (indices in NCB)
# SFPNT&SFPTT: Selective Feature preserving nodes and triangles (indices in NCT and ConnectT) on target mesh.
# k_max: maximum number of iterations
# 1) The base mesh is first morphed into the target using 1 to 1 correspondence with target mesh Landmarks.
# 2) Elastic surface registration is done using FDNB&SFPNT to target and base mesh respectively
# if FDNB is displaced to a triangle other than SFPTT, displacement of concern is discarded in order
# to retain only selected features.
######## ADDITIONAL SETTINGS REQUIRED ARE SET INTERNAL TO CODE #########
print
print "SELECTIVE MESH MORPHING ALGORITHM USING ELASTIC SURFACE REGISTRATION"
print " -G.J.J.v.Rensburg - 22/04/2010-"
t_start = time.clock()
ConnectB = np.array(ConnectB, int)
ConnectT = np.array(ConnectT, int)
LandmB = np.array(
LandmB[:, 0], int
) # do -1 later to be consistent with python indexing, first need to do other "temporary landmarks"& check that they dont fall on actual landmark positions!
LandmT = np.array(LandmT[:, 0], int)
# Settings for elastic surface registration:
m = 10 # nearest neighbour parameter
alph = 0.5 # normilization factor
gamm = 2 # smoothing parameter1
sigm0 = 10 # smoothing parameter2
f = 1.0715 # smoothing parameter3
Tol = 0.0001 # stopping criteria
# determine N1,N2,T1 and T2:
N1 = np.array(np.shape(NCB))[0, ]
N2 = np.array(np.shape(NCT))[0, ]
T1 = np.array(np.shape(ConnectB))[0, ]
T2 = np.array(np.shape(ConnectT))[0, ]
NL = np.array(np.shape(LandmB))[0, ]
################################ INITIALIZE & NODES OF CONCERN: #################################
########################################################################################################
print
print "INITIALIZE SURFACE DEFORMATION"
k = 1
CONV = np.zeros((k_max, 1))
print " enquire nodes where required displacement is checked"
# remove Landmarks from FDNB and SFPNT:
for i in range(0, NL):
if find_repeats(np.r_[FDNB, LandmB[i, ]])[0].size > 0:
r = np.where(FDNB == LandmB[i, ])[0]
FDNB = np.r_[FDNB[0:r, ], FDNB[r + 1:FDNB.size, ]]
if find_repeats(np.r_[SFPNT, LandmT[i, ]])[0].size > 0:
r = np.where(SFPNT == LandmT[i, ])[0]
SFPNT = np.r_[SFPNT[0:r, ], SFPNT[r + 1:SFPNT.size, ]]
SamplingB = FDNB.size
SamplingT = SFPNT.size
LMB = np.r_[
FDNB,
LandmB] # Last NL entries are reserved for Landmarks that HAVE TO FIT points on the target mesh
LMT = np.r_[SFPNT, LandmT]
print " Compute known displacement for Base_Landmark to Target_Landmark"
knownC = NCB[LandmB, ]
knownD = NCT[LandmT, ] - knownC
print
print "COARSE SURFACE REGISTRATION"
print " using landmark displacements to deform using RBF"
W_km1 = RBFmorph(NCB, NCB[LandmB, ], NCT[LandmT, ] - NCB[LandmB])
################################ MAIN MESH DEFORMATION ALGORITHM: #################################
########################################################################################################
print
print "ELASTIC SURFACE REGISTRATION"
#Compute target-mesh triangle centroids:
print "determining centroids of target surface triangles"
S_2_centr = np.c_[np.sum(
np.c_[NCT[ConnectT[:, 0], 0], NCT[ConnectT[:, 1], 0],
NCT[ConnectT[:, 2], 0]], 1) / 3,
np.sum(
np.c_[NCT[ConnectT[:, 0], 1], NCT[ConnectT[:, 1], 1],
NCT[ConnectT[:, 2], 1]], 1) / 3,
np.sum(
np.c_[NCT[ConnectT[:, 0], 2], NCT[ConnectT[:, 1], 2],
NCT[ConnectT[:, 2], 2]], 1) / 3]
print "determining kd-trees of target surface centroids and nodal coordinates"
KDT_TC = KDTree(S_2_centr, m)
KDT_TN = KDTree(NCT, m)
while k <= k_max:
D1 = np.zeros((SamplingB, 3))
D2 = np.zeros((SamplingT, 3))
DS = np.zeros((N1, 3))
print
print "MESH DEFORMATION ITERATION", k
print "determining known displacement of landmarks"
knownD = NCT[LandmT, ] - W_km1[LandmB, ]
print " determining centroids of deforming mesh"
W_km1_centr = np.c_[
np.sum(
np.c_[W_km1[ConnectB[:, 0], 0], W_km1[ConnectB[:, 1], 0],
W_km1[ConnectB[:, 2], 0]], 1) / 3,
np.sum(
np.c_[W_km1[ConnectB[:, 0], 1], W_km1[ConnectB[:, 1], 1],
W_km1[ConnectB[:, 2], 1]], 1) / 3,
np.sum(
np.c_[W_km1[ConnectB[:, 0], 2], W_km1[ConnectB[:, 1], 2],
W_km1[ConnectB[:, 2], 2]], 1) / 3]
print " determining kd-tree of current deforming surface centroids and nodal coordinates"
KDT_KC = KDTree(W_km1_centr, m)
KDT_KN = KDTree(W_km1, m)
print " setting up D1(i,d)"
tic = time.clock()
for i in range(0, SamplingB):
nn = LMB[i]
# query kd-tree for closest triangle to node:
ncl = KDT_TC.query(W_km1[nn, :])[1]
# check if
if np.where(SFPTT == ncl)[0].size > 0:
## determine target triangle normal vector:
#tnorm = np.cross(NCT[ConnectT[ncl,1],:]-NCT[ConnectT[ncl,0],:],NCT[ConnectT[ncl,2],:]-NCT[ConnectT[ncl,0],:])
#tnorm = tnorm/np.sqrt(np.sum(tnorm*tnorm))
## determine current vertex normal
#vnorm=vertexnormal(W_km1,ConnectB[np.where(ConnectB==nn)[0],])
#if np.dot(vnorm[nn,],tnorm)>0: #check for correlation between closest triangle directional normal&base-mesh curvature
## move to triangle / closest node
D1[i, :] = Ndisp(W_km1[nn, :], ncl, NCT, ConnectT, S_2_centr,
KDT_TN)
D1 = np.r_[D1, knownD]
print " ", time.clock() - tic, " seconds"
print " setting up D2(j,c)"
tic = time.clock()
for j in range(0, SamplingT):
nn = LMT[j]
ncl = KDT_KC.query(NCT[nn, :])[1]
#tnorm = np.cross(W_km1[ConnectB[ncl,1],:]-W_km1[ConnectB[ncl,0],:],W_km1[ConnectB[ncl,2],:]-W_km1[ConnectB[ncl,0],:])
#tnorm = tnorm/np.sqrt(np.sum(tnorm*tnorm))
#vnorm=vertexnormal(NCT,ConnectT[np.where(ConnectT==nn)[0],])
#if np.dot(vnorm[nn,],tnorm)>0:
D2[j, :] = Ndisp(NCT[nn, :], ncl, W_km1, ConnectB, W_km1_centr,
KDT_KN)
#else:
#D2[j,:] = np.array([0,0,0])
D2 = np.r_[D2, -knownD]
print " ", time.clock() - tic, " seconds"
# Compute displacement update for each node using suggested Gaussian radial basis function:
print " determining smoothed displacement field"
tic = time.clock()
# Deform mesh using Gaussian smoothing as suggested in paper by R.Bryan et al.
sigma_k2 = np.power(np.power(f, -k) * sigm0, 2)
for nodes in range(0, N1):
G1node = np.array([W_km1[nodes, :]]).T * np.ones(
(1, SamplingB + NL)) - W_km1[LMB, :].T
G1node = np.exp(-np.sum(G1node * G1node, 0) / sigma_k2)
G2node = np.array([W_km1[nodes, :]]).T * np.ones(
(1, SamplingT + NL)) - NCT[LMT, :].T - D2.T
G2node = np.exp(-np.sum(G2node * G2node, 0) / sigma_k2)
DS[nodes, :] = (
np.sum(D1.T * G1node, 1) / np.sum(G1node, 0) -
np.sum(D2.T * G2node, 1) / np.sum(G2node, 0)) / gamm
print " ", time.clock() - tic, " seconds"
# determine wheter convergence is acheived
TotalMorph = np.sum(np.sqrt(np.sum(DS * DS, 1)), 0)
print " total displacement for current deformation iteration:"
print TotalMorph
if (TotalMorph < Tol):
print
print "CONVERGED SOLUTION OBTAINED"
CONV[k - 1, 0] = TotalMorph
k = k_max * 10 + 1
W_km1 = W_km1 + DS
elif (k < 10) | (TotalMorph <= CONV[0, ]):
print "problem not yet converged at iteration", k
CONV[k - 1, 0] = TotalMorph
k = k + 1
# Deform mesh:
print " deforming mesh (update of W_{k-1})"
W_km1 = W_km1 + DS
else:
print "PROBLEM DIVERGING"
k = k_max * 10 - 1
if (k > 1) & (np.mod(k - 1, 10) == 0):
print
print "Do 3 iterations of Laplacian Smoothing to improve element quality"
tic = time.clock()
W_km1 = LaplacianSmooth(W_km1, ConnectB, 3)
print " Smoothing done in ", time.clock() - tic, " seconds"
print "COARSE SURFACE REGISTRATION"
print " using landmark displacements to deform using RBF"
W_km1 = RBFmorph(W_km1, W_km1[LandmB, ],
NCT[LandmT, ] - W_km1[LandmB, ])
print
if k == k_max + 1:
print
print "SOLUTION TERMINATED: maximum iterations,(", k_max, ") reached"
print
print "TOTAL TIME FOR ELASTIC SURFACE REGISTRATION : ", time.clock(
) - t_start, "seconds"
return W_km1, CONV
