def endOfIteration(self):
#print self.obj0
self.iter += 1
if (self.iter % self.saveRate) == 0:
print 'saving...'
(obj1, self.ct, self.St, self.grt, self.Jt) = self.objectiveFunDef(self.at, self.Afft, withTrajectory=True)
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]
(ct, St, grt) = evol.gaussianDiffeonsEvolutionEuler(self.c0, self.S0, self.at, self.param.sigmaKernel, affine=A, withPointSet= self.gr0Fine)
# (ct, St, grt, Jt) = evol.gaussianDiffeonsEvolutionEuler(self.c0, self.S0, self.at, self.param.sigmaKernel, affine=A,
# withPointSet = self.fv0Fine.vertices, withJacobian=True)
imDef = diffeo.gridScalars(grid = self.im1)
for kk in range(self.Tsize+1):
imDef.data = diffeo.multilinInterp(self.im1.data, grt[kk, ...].transpose(range(-1, self.grt.ndim-2)))
imDef.saveImg(self.outputDir +'/'+ self.saveFile+str(kk)+'.png', normalize=True)
if self.dim==3:
gd.saveDiffeons(self.outputDir +'/'+ self.saveFile+'Diffeons'+str(kk)+'.vtk', self.ct[kk,...], self.St[kk,...])
elif self.dim==2:
(R, detR) = gd.multiMatInverse1(self.St[kk,...], isSym=True)
diffx = self.gr1[..., np.newaxis, :] - self.ct[kk, ...]
betax = (R*diffx[..., np.newaxis, :]).sum(axis=-1)
dst = (betax * diffx).sum(axis=-1)
diffIm = np.minimum((255*(1-dst)*(dst < 1)).astype(float).sum(axis=-1), 255)
out = Image.fromarray(diffIm.astype(np.uint8))
out.save(self.outputDir +'/'+ self.saveFile+'Diffeons'+str(kk)+'.png')
else:
(obj1, self.ct, self.St, self.grt, self.Jt) = self.objectiveFunDef(self.at, self.Afft, withTrajectory=True)
def endOfIteration(self):
#print self.obj0
self.iter += 1
if (self.iter % self.saveRate == 0) :
if self.dcurr:
print 'saving...'
(obj1, self.ct, self.St, self.bt, self.xt, self.xSt, Jt) = self.objectiveFunDef(self.at, self.Afft, withTrajectory=True, withJacobian=True)
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]
(ct, St, xt, Jt) = evol.gaussianDiffeonsEvolutionEuler(self.c0, self.S0, self.at, self.param.sigmaKernel, affine=A,
withPointSet = self.fv0Fine.vertices, withJacobian=True)
fvDef = surfaces.Surface(surf=self.fv0Fine)
for kk in range(self.Tsize+1):
self.fvDef.updateVertices(np.squeeze(self.xt[kk, :, :]))
fvDef.updateVertices(np.squeeze(xt[kk, :, :]))
# foo = (gd.diffeonCurrentNormDef(self.xt[kk], self.xSt[kk], self.bt[kk], self.fvDef, self.param.KparDist.sigma)
# + gd.diffeonCurrentNorm0(self.fvDef, self.param.KparDist))/ (self.param.sigmaError**2)
# print foo
fvDef.saveVTK(self.outputDir +'/'+ self.saveFile+str(kk)+'.vtk', scalars = Jt[kk, :], scal_name='Jacobian')
gd.saveDiffeons(self.outputDir +'/'+ self.saveFile+'Diffeons'+str(kk)+'.vtk', self.ct[kk,:,:], self.St[kk,:,:,:])
self.saveB(self.outputDir +'/'+ self.saveFile+'Bt'+str(kk)+'.vtk', self.xt[kk,:,:], self.bt[kk,:,:])
else:
(obj1, self.ct, self.St, self.xt) = self.objectiveFunDef(self.at, self.Afft, withTrajectory=True)
self.fvDef.updateVertices(np.squeeze(self.xt[-1, :, :]))
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]
(ct, St, xt, Jt) = evol.gaussianDiffeonsEvolutionEuler(self.c0, self.S0, self.at, self.param.sigmaKernel, affine=A,
withPointSet = self.fv0Fine.vertices, withJacobian=True)
fvDef = surfaces.Surface(surf=self.fv0Fine)
for kk in range(self.Tsize+1):
fvDef.updateVertices(np.squeeze(xt[kk, :, :]))
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', scalars = self.idx, scal_name='Labels')
gd.saveDiffeons(self.outputDir +'/'+ self.saveFile+'Diffeons'+str(kk)+'.vtk', self.ct[kk,:,:], self.St[kk,:,:,:])
#print self.bt
else:
if self.dcurr:
(obj1, self.ct, self.St, self.bt, self.xt, self.xSt) = self.objectiveFunDef(self.at, self.Afft, withTrajectory=True)
else:
(obj1, self.ct, self.St, self.xt) = self.objectiveFunDef(self.at, self.Afft, withTrajectory=True)
self.fvDef.updateVertices(np.squeeze(self.xt[-1, :, :]))
