def printResults(self,Jt):
nn = 0 ;
yt0 = [] ;
for k in range(self.ncurve):
if self.dim==2:
A = self.affB.getTransforms(self.Afft[k])
(xt,yt) = evol.landmarkDirectEvolutionEuler(self.x0[k], self.at[k], self.param.KparDiff, affine=A, withPointSet=self.gridxy[k])
yt0.append(yt)
#print xt.shape, yt.shape
n1 = self.xt[k].shape[1] ;
for kk in range(self.Tsize+1):
self.fvDef[k].updateVertices(np.squeeze(self.xt[-1][kk, nn:nn+n1, :]))
self.fvDef[k].saveVTK(self.outputDir +'/'+ self.saveFile+str(k)+'Out'+str(kk)+'.vtk', scalars = Jt[-1][kk, nn:nn+n1], scal_name='Jacobian')
self.fvDef[k].updateVertices(np.squeeze(self.xt[k][kk, :, :]))
self.fvDef[k].saveVTK(self.outputDir +'/'+self.saveFile+str(k)+'In'+str(kk)+'.vtk', scalars = Jt[k][kk, :], scal_name='Jacobian')
if self.dim == 2:
self.gridDef[k].vertices = np.copy(yt[kk, :, :])
self.gridDef[k].saveVTK(self.outputDir +'/grid'+str(k)+'In'+str(kk)+'.vtk')
nn += n1
#print xt.shape, yt.shape
I1 = np.nonzero(self.inGrid[-1])
if self.dim==2:
(xt,yt) = evol.landmarkDirectEvolutionEuler(self.x0[self.ncurve], self.at[self.ncurve], self.param.KparDiffOut, withPointSet=self.gridxy[-1])
yt0.append(yt)
for kk in range(self.Tsize+1):
self.gridDef[-1].vertices = np.copy(yt[kk, :, :])
self.gridDef[-1].saveVTK(self.outputDir +'/gridOut'+str(kk)+'.vtk')
for k in range(self.ncurve+1):
I1 = np.nonzero(self.inGrid[k])
self.gridAll.vertices[I1] = np.copy(yt0[k][kk, ...])
self.gridAll.saveVTK(self.outputDir +'/gridAll'+str(kk)+'.vtk')
def objectiveFunDef(self, at, Afft, withTrajectory = False, withJacobian=False, x0 = None):
if x0 == None:
x0 = self.fv0.vertices
param = self.param
timeStep = 1.0/self.Tsize
#dim2 = self.dim**2
A = self.affB.getTransforms(Afft)
# A = [np.zeros([self.Tsize, self.dim, self.dim]), np.zeros([self.Tsize, self.dim])]
# if self.affineDim > 0:
# for t in range(self.Tsize):
# AB = np.dot(self.affineBasis, Afft[t])
# A[0][t] = AB[0:dim2].reshape([self.dim, self.dim])
# A[1][t] = AB[dim2:dim2+self.dim]
if withJacobian:
(xt,Jt) = evol.landmarkDirectEvolutionEuler(x0, at, param.KparDiff, affine=A, withJacobian=True)
else:
xt = evol.landmarkDirectEvolutionEuler(x0, at, param.KparDiff, affine=A)
#print xt[-1, :, :]
#print obj
obj=0
for t in range(self.Tsize):
z = np.squeeze(xt[t, :, :])
a = np.squeeze(at[t, :, :])
#rzz = kfun.kernelMatrix(param.KparDiff, z)
ra = param.KparDiff.applyK(z, a)
obj = obj + self.regweight*timeStep*np.multiply(a, (ra)).sum()
if self.affineDim > 0:
obj += timeStep * np.multiply(self.affineWeight.reshape(Afft[t].shape), Afft[t]**2).sum()
#print xt.sum(), at.sum(), obj
if withJacobian:
return obj, xt, Jt
elif withTrajectory:
return obj, xt
else:
return obj
def endOptim(self):
if self.saveRate==0 or self.iter%self.saveRate > 0:
if self.dim==2:
A = self.affB.getTransforms(self.Afft)
(xt,yt) = evol.landmarkDirectEvolutionEuler(self.fv0.vertices, self.at, self.param.KparDiff, affine=A, withPointSet=self.gridxy)
for kk in range(self.Tsize+1):
self.fvDef.updateVertices(np.squeeze(self.xt[kk, :, :]))
#self.fvDef.saveVTK(self.outputDir +'/'+ self.saveFile+str(kk)+'.vtk', scalars = Jt[kk, :], scal_name='Jacobian')
self.fvDef.saveVTK(self.outputDir +'/'+ self.saveFile+str(kk)+'.vtk')
self.defCost = self.obj - self.obj0 - self.dataTerm(self.fvDef)
def objectiveFunDef(self, at, Afft, withTrajectory = False, withJacobian = False):
param = self.param
timeStep = 1.0/at.shape[0]
dim2 = self.dim**2
A = [np.zeros([self.Tsize, self.dim, self.dim]), np.zeros([self.Tsize, self.dim])]
if self.affineDim > 0:
for t in range(self.Tsize):
AB = np.dot(self.affineBasis, Afft[t])
A[0][t] = AB[0:dim2].reshape([self.dim, self.dim])
A[1][t] = AB[dim2:dim2+self.dim]
if withJacobian:
xJ = evol.landmarkDirectEvolutionEuler(self.fv0.vertices, at, param.KparDiff, withJacobian = True, affine=A)
xt = xJ[0]
Jt = xJ[1]
else:
xt = evol.landmarkDirectEvolutionEuler(self.fv0.vertices, at, param.KparDiff, affine=A)
obj=0
for t in range(at.shape[0]):
z = np.squeeze(xt[t, :, :])
a = np.squeeze(at[t, :, :])
ra = self.param.KparDiff.applyK(z, a)
obj += self.regweight*timeStep*np.multiply(a, ra).sum()
if self.affineDim > 0:
obj += timeStep * np.multiply(self.affineWeight.reshape(Afft[t].shape), Afft[t]**2).sum()
cstr = [[], []]
if self.nconstr > 0:
cstr = self.constraintTerm(xt)
obj += cstr[0]
#print xt.sum(), at.sum(), obj
if withJacobian:
return obj, xt, Jt, cstr[1]
elif withTrajectory:
return obj, xt, cstr[1]
else:
return obj
def endOfIteration(self):
(obj1, self.xt, Jt) = self.objectiveFunDef(self.at, self.Afft, withTrajectory=True, withJacobian=True)
self.iter += 1
if self.saveRate > 0 and self.iter%self.saveRate==0:
if self.dim==2:
A = self.affB.getTransforms(self.Afft)
(xt,yt) = evol.landmarkDirectEvolutionEuler(self.fv0.vertices, self.at, self.param.KparDiff, affine=A, withPointSet=self.gridxy)
for kk in range(self.Tsize+1):
self.fvDef.updateVertices(np.squeeze(self.xt[kk, :, :]))
#self.fvDef.saveVTK(self.outputDir +'/'+ self.saveFile+str(kk)+'.vtk', scalars = Jt[kk, :], scal_name='Jacobian')
self.fvDef.saveVTK(self.outputDir +'/'+ self.saveFile+str(kk)+'.vtk')
if self.dim == 2:
self.gridDef.vertices = np.copy(yt[kk, :, :])
self.gridDef.saveVTK(self.outputDir +'/grid'+str(kk)+'.vtk')
else:
self.fvDef.updateVertices(np.squeeze(self.xt[self.Tsize, :, :]))
def covectorEvolution(self, at, Afft, px1):
N = self.npt
dim = self.dim
M = self.Tsize
timeStep = 1.0/M
dim2 = self.dim**2
A = [np.zeros([self.Tsize, self.dim, self.dim]), np.zeros([self.Tsize, self.dim])]
if self.affineDim > 0:
for t in range(self.Tsize):
AB = np.dot(self.affineBasis, Afft[t])
A[0][t] = AB[0:dim2].reshape([self.dim, self.dim])
A[1][t] = AB[dim2:dim2+self.dim]
xt = evol.landmarkDirectEvolutionEuler(self.x0, at, self.param.KparDiff, affine=A)
#### Restart here
pxt = np.zeros([M, N, dim])
if self.nconstr > 0:
(lmb, dxcval) = self.constraintTermGrad(xt)
pxt[M-1, :, :] = px1 + dxcval[M] *timeStep
else:
pxt[M-1, :, :] = px1
# print c
for t in range(M-1):
px = np.squeeze(pxt[M-t-1, :, :])
z = np.squeeze(xt[M-t-1, :, :])
a = np.squeeze(at[M-t-1, :, :])
if self.nconstr > 0:
zpx = np.copy(dxcval[M-t-1])
else:
zpx = np.zeros(px1.shape)
a1 = [px, a, -2*self.regweight*a]
a2 = [a, px, a]
zpx += self.param.KparDiff.applyDiffKT(z, a1, a2)
if self.affineDim > 0:
zpx += np.dot(px, A[0][M-t-1])
pxt[M-t-2, :, :] = np.squeeze(pxt[M-t-1, :, :]) + timeStep * zpx
return pxt, xt
def covectorEvolution(self, at, Afft, px1):
M = self.Tsize
timeStep = 1.0/M
dim2 = self.dim**2
A = [np.zeros([self.Tsize, self.dim, self.dim]), np.zeros([self.Tsize, self.dim])]
if self.affineDim > 0:
for t in range(self.Tsize):
AB = np.dot(self.affineBasis, Afft[t])
A[0][t] = AB[0:dim2].reshape([self.dim, self.dim])
A[1][t] = AB[dim2:dim2+self.dim]
xt = evol.landmarkDirectEvolutionEuler(self.x0, at, self.param.KparDiff, affine = A)
#xt = xJ
pxt = np.zeros([M+1, self.npt, self.dim])
pxt[M, :, :] = px1
foo = self.constraintTermGrad(xt, at, Afft)
lmb = foo[0]
dxcval = foo[1]
dacval = foo[2]
dAffcval = foo[3]
pxt[M, :, :] += timeStep * dxcval[M]
for t in range(M):
px = np.squeeze(pxt[M-t, :, :])
z = np.squeeze(xt[M-t-1, :, :])
a = np.squeeze(at[M-t-1, :, :])
zpx = np.copy(dxcval[M-t-1])
a1 = np.concatenate((px[np.newaxis,...], a[np.newaxis,...], -2*self.regweight*a[np.newaxis,...]))
a2 = np.concatenate((a[np.newaxis,...], px[np.newaxis,...], a[np.newaxis,...]))
zpx += self.param.KparDiff.applyDiffKT(z, a1, a2)
if self.affineDim > 0:
zpx += np.dot(px, A[0][M-t-1])
pxt[M-t-1, :, :] = px + timeStep * zpx
return pxt, xt, dacval, dAffcval
def endOfIteration(self):
self.iter += 1
if self.iter >= self.affBurnIn:
self.coeffAff = self.coeffAff2
if (self.iter % self.saveRate == 0):
logging.info('Saving surfaces...')
(obj1, self.xt) = self.objectiveFunDef(self.at, self.Afft, withTrajectory=True)
for k in range(self.nTarg):
self.fvDef[k].updateVertices(np.squeeze(self.xt[(k+1)*self.Tsize1, :, :]))
dim2 = self.dim**2
A = [np.zeros([self.Tsize, self.dim, self.dim]), np.zeros([self.Tsize, self.dim])]
if self.affineDim > 0:
for t in range(self.Tsize):
AB = np.dot(self.affineBasis, self.Afft[t])
A[0][t] = AB[0:dim2].reshape([self.dim, self.dim])
A[1][t] = AB[dim2:dim2+self.dim]
(xt, ft, Jt) = evol.landmarkDirectEvolutionEuler(self.x0, self.at, self.param.KparDiff, affine=A,
withPointSet = self.fv0Fine.vertices, withJacobian=True)
if self.affine=='euclidean' or self.affine=='translation':
f = surfaces.Surface(surf=self.fv0Fine)
X = self.affB.integrateFlow(self.Afft)
displ = np.zeros(self.x0.shape[0])
dt = 1.0 /self.Tsize ;
for t in range(self.Tsize+1):
U = la.inv(X[0][t])
yyt = np.dot(xt[t,...] - X[1][t, ...], U.T)
zt = np.dot(ft[t,...] - X[1][t, ...], U.T)
if t < self.Tsize:
at = np.dot(self.at[t,...], U.T)
vt = self.param.KparDiff.applyK(yyt, at, firstVar=zt)
f.updateVertices(zt)
vf = surfaces.vtkFields() ;
vf.scalars.append('Jacobian') ;
vf.scalars.append(np.exp(Jt[t, :])-1)
vf.scalars.append('displacement')
vf.scalars.append(displ)
vf.vectors.append('velocity') ;
vf.vectors.append(vt)
nu = self.fv0ori*f.computeVertexNormals()
displ += dt * (vt*nu).sum(axis=1)
f.saveVTK2(self.outputDir +'/'+self.saveFile+'Corrected'+str(t)+'.vtk', vf)
for k,fv in enumerate(self.fv1):
f = surfaces.Surface(surf=fv)
U = la.inv(X[0][(k+1)*self.Tsize1])
yyt = np.dot(f.vertices - X[1][(k+1)*self.Tsize1, ...], U.T)
f.updateVertices(yyt)
f.saveVTK(self.outputDir +'/Target'+str(k)+'Corrected.vtk')
fvDef = surfaces.Surface(surf=self.fv0Fine)
AV0 = fvDef.computeVertexArea()
nu = self.fv0ori*self.fv0Fine.computeVertexNormals()
#v = self.v[0,...]
displ = np.zeros(self.npt)
dt = 1.0 /self.Tsize ;
v = self.param.KparDiff.applyK(ft[0,...], self.at[0,...], firstVar=self.xt[0,...])
for kk in range(self.Tsize+1):
fvDef.updateVertices(np.squeeze(ft[kk, :, :]))
AV = fvDef.computeVertexArea()
AV = (AV[0]/AV0[0])-1
vf = surfaces.vtkFields() ;
vf.scalars.append('Jacobian') ;
vf.scalars.append(np.exp(Jt[kk, :])-1)
vf.scalars.append('Jacobian_T') ;
vf.scalars.append(AV[:,0])
vf.scalars.append('Jacobian_N') ;
vf.scalars.append(np.exp(Jt[kk, :])/(AV[:,0]+1)-1)
vf.scalars.append('displacement')
vf.scalars.append(displ)
displ += dt * (v*nu).sum(axis=1)
if kk < self.Tsize:
nu = self.fv0ori*fvDef.computeVertexNormals()
v = self.param.KparDiff.applyK(ft[kk,...], self.at[kk,...], firstVar=self.xt[kk,...])
#v = self.v[kk,...]
kkm = kk
else:
kkm = kk-1
vf.vectors.append('velocity') ;
vf.vectors.append(self.v[kkm,:])
fvDef.saveVTK2(self.outputDir +'/'+ self.saveFile+str(kk)+'.vtk', vf)
else:
(obj1, self.xt) = self.objectiveFunDef(self.at, self.Afft, withTrajectory=True)
for k in range(self.nTarg):
self.fvDef[k].updateVertices(np.squeeze(self.xt[(k+1)*self.Tsize1, :, :]))
def covectorEvolution(self, at, Afft, px1, pnu1):
M = self.Tsize
timeStep = 1.0/M
xt = []
nut = []
pxt = []
pnut = []
A = []
dim2 = self.dim**2
for k in range(self.ncurve):
A.append([np.zeros([self.Tsize, self.dim, self.dim]), np.zeros([self.Tsize, self.dim])])
if self.affineDim > 0:
for t in range(self.Tsize):
AB = np.dot(self.affineBasis, Afft[k][t])
A[k][0][t] = AB[0:dim2].reshape([self.dim, self.dim])
A[k][1][t] = AB[dim2:dim2+self.dim]
xJ = evol.landmarkDirectEvolutionEuler(self.x0[k], at[k], self.param.KparDiff, withNormals = self.nu0[k], affine = A[k])
xt.append(xJ[0])
nut.append(xJ[1])
pxt.append(np.zeros([M, self.npt[k], self.dim]))
pnut.append(np.zeros([M, self.npt[k], self.dim]))
#print pnu1[k].shape
pxt[k][M-1, :, :] = px1[k]
pnut[k][M-1] = pnu1[k]
xt.append(evol.landmarkDirectEvolutionEuler(self.x0[self.ncurve], at[self.ncurve], self.param.KparDiffOut))
pxt.append(np.zeros([M, self.npoints, self.dim]))
pxt[self.ncurve][M-1, :, :] = px1[self.ncurve]
#lmb = np.zeros([self.npoints, self.dim])
foo = self.constraintTermGrad(xt, nut, at, Afft)
lmb = foo[0]
dxcval = foo[1]
dacval = foo[2]
dAffcval = foo[3]
for k in range(self.ncurve):
pxt[k][M-1, :, :] += timeStep * dxcval[k][M]
pxt[self.ncurve][M-1, :, :] += timeStep * dxcval[self.ncurve][M]
for t in range(M-1):
npt = 0
for k in range(self.ncurve):
npt1 = npt + self.npt[k]
px = np.squeeze(pxt[k][M-t-1, :, :])
z = np.squeeze(xt[k][M-t-1, :, :])
a = np.squeeze(at[k][M-t-1, :, :])
zpx = np.copy(dxcval[k][M-t-1])
a1 = np.concatenate((px[np.newaxis,...], a[np.newaxis,...], -2*self.regweight*a[np.newaxis,...]))
a2 = np.concatenate((a[np.newaxis,...], px[np.newaxis,...], a[np.newaxis,...]))
zpx += self.param.KparDiff.applyDiffKT(z, a1, a2)
if self.affineDim > 0:
zpx += np.dot(px, A[k][0][M-t-1])
pxt[k][M-t-2, :, :] = np.squeeze(pxt[k][M-t-1, :, :]) + timeStep * zpx
npt = npt1
px = np.squeeze(pxt[self.ncurve][M-t-1, :, :])
z = np.squeeze(xt[self.ncurve][M-t-1, :, :])
a = np.squeeze(at[self.ncurve][M-t-1, :, :])
zpx = np.copy(dxcval[self.ncurve][M-t-1])
a1 = np.concatenate((px[np.newaxis,...], a[np.newaxis,...], -2*self.regweightOut*a[np.newaxis,...]))
a2 = np.concatenate((a[np.newaxis,...], px[np.newaxis,...], a[np.newaxis,...]))
zpx += self.param.KparDiffOut.applyDiffKT(z, a1, a2)
pxt[self.ncurve][M-t-2, :, :] = np.squeeze(pxt[self.ncurve][M-t-1, :, :]) + timeStep * zpx
return pxt, pnut, xt, nut, dacval, dAffcval
def objectiveFunDef(self, at, Afft, withTrajectory = False, withJacobian = False):
param = self.param
timeStep = 1.0/self.Tsize
xt = []
nut = []
dim2 = self.dim**2
if withJacobian:
Jt = []
for k in range(self.ncurve):
A = [np.zeros([self.Tsize, self.dim, self.dim]), np.zeros([self.Tsize, self.dim])]
if self.affineDim > 0:
for t in range(self.Tsize):
AB = np.dot(self.affineBasis, Afft[k][t])
A[0][t] = AB[0:dim2].reshape([self.dim, self.dim])
A[1][t] = AB[dim2:dim2+self.dim]
xJ = evol.landmarkDirectEvolutionEuler(self.x0[k], at[k], param.KparDiff, affine = A, withNormals = self.nu0[k], withJacobian = True)
xt.append(xJ[0])
nut.append(xJ[1])
Jt.append(xJ[2])
xJ = evol.landmarkDirectEvolutionEuler(self.x0[self.ncurve], at[self.ncurve], param.KparDiffOut, withJacobian=True)
xt.append(xJ[0])
Jt.append(xJ[1])
else:
for k in range(self.ncurve):
A = [np.zeros([self.Tsize, self.dim, self.dim]), np.zeros([self.Tsize, self.dim])]
if self.affineDim > 0:
for t in range(self.Tsize):
AB = np.dot(self.affineBasis, Afft[k][t])
A[0][t] = AB[0:dim2].reshape([self.dim, self.dim])
A[1][t] = AB[dim2:dim2+self.dim]
xJ = evol.landmarkDirectEvolutionEuler(self.x0[k], at[k], param.KparDiff, withNormals = self.nu0[k], affine = A)
xt.append(xJ[0])
nut.append(xJ[1])
xt.append(evol.landmarkDirectEvolutionEuler(self.x0[self.ncurve], at[self.ncurve], param.KparDiffOut))
#print xt[-1, :, :]
#print obj
obj=0
for t in range(self.Tsize):
zB = np.squeeze(xt[self.ncurve][t, :, :])
for k in range(self.ncurve):
z = np.squeeze(xt[k][t, :, :])
a = np.squeeze(at[k][t, :, :])
ra = param.KparDiff.applyK(z,a)
obj += self.regweight*timeStep*np.multiply(a, ra).sum()
if self.affineDim > 0:
obj += timeStep * np.multiply(self.affineWeight.reshape(Afft[k][t].shape), Afft[k][t]**2).sum()
#print t,k,obj
a = np.squeeze(at[self.ncurve][t, :, :])
ra = param.KparDiffOut.applyK(zB,a)
obj += self.regweightOut*timeStep*np.multiply(a, ra).sum()
#print 'obj before constraints:', obj
cstr = self.constraintTerm(xt, nut, at, Afft)
obj += cstr[0]
if withJacobian:
return obj, xt, Jt, cstr[1]
elif withTrajectory:
return obj, xt, cstr[1]
else:
return obj