# # Solve for the TPS based off of the landmakrs
# spline = SolveSpline(flipLM)
# h = SplineToHField(spline, T2Grid, memT)
# print ca.MinMax(h)
# liveDef = T2.copy()
# cc.ApplyHReal(liveDef,live,h)
# Variance equalize the volumes and blur the live
T2_VE = ca.Image3D(T2.grid(), memT)
live_VE = ca.Image3D(liveDef.grid(), memT)
ca.Copy(T2_VE, T2)
cc.VarianceEqualize_I(T2_VE, sigma=5)
ca.Copy(live_VE, liveDef)
cc.VarianceEqualize_I(live_VE, sigma=5)
gausfilt = ca.GaussianFilterGPU()
gausfilt.updateParams(live_VE.size(), ca.Vec3Df(3, 3, 3), ca.Vec3Di(3, 3, 3))
live_VEfilt = ca.Image3D(live_VE.grid(), memT)
temp = ca.Image3D(live_VE.grid(), memT)
gausfilt.filter(live_VEfilt, live_VE, temp)
dispslice = [128, 120, 128]
# Display some initial images
cd.Disp3Pane(live_VEfilt,
rng=[-3, 3],
sliceIdx=dispslice,
title='Live VE Filtered')
cd.Disp3Pane(T2_VE, rng=[-3, 3], sliceIdx=dispslice, title='T2 VE')
print 'MinMax of Live = ' + str(ca.MinMax(live_VE))
print 'MinMax of T2 = ' + str(ca.MinMax(T2_VE))
preRegDiff = T2_VE - live_VEfilt
def DefReg(I_src, I_tar, config, memT, idConf):
I_src.toType(memT)
I_tar.toType(memT)
# Convert to 2D spacing (because it really matters)
sp2D = I_src.spacing().tolist()
sp2D = ca.Vec3Df(sp2D[0], sp2D[1], 1)
I_tar.setSpacing(sp2D)
I_src.setSpacing(sp2D)
gridReg = I_tar.grid()
# Blur the images
I_tar_blur = I_tar.copy()
I_src_blur = I_src.copy()
temp = ca.Image3D(I_tar.grid(), memT)
gausFilt = ca.GaussianFilterGPU()
scaleList = config.scale
# Initiate the scale manager
scaleManager = ca.MultiscaleManager(gridReg)
for s in scaleList:
scaleManager.addScaleLevel(s)
if memT == ca.MEM_HOST:
resampler = ca.MultiscaleResamplerGaussCPU(gridReg)
else:
resampler = ca.MultiscaleResamplerGaussGPU(gridReg)
# Generate the scratch images
scratchITar = ca.Image3D(gridReg, memT)
scratchISrc = ca.Image3D(gridReg, memT)
scratchI = ca.Image3D(gridReg, memT)
scratchF = ca.Field3D(gridReg, memT)
compF = ca.Field3D(gridReg, memT)
def SetScale(scale):
'''Scale Management for Multiscale'''
scaleManager.set(scale)
resampler.setScaleLevel(scaleManager)
curGrid = scaleManager.getCurGrid()
curGrid.spacing().z = 1 # Because only 2D
print 'Inside setScale(). Current grid is ', curGrid
if scaleManager.isLastScale():
print 'Inside setScale(): **Last Scale**'
if scaleManager.isFirstScale():
print 'Inside setScale(): **First Scale**'
scratchISrc.setGrid(curGrid)
scratchITar.setGrid(curGrid)
scratchI.setGrid(curGrid)
compF.setGrid(curGrid)
idConf.study.I0 = ca.Image3D(curGrid, memT)
idConf.study.I1 = ca.Image3D(curGrid, memT)
if scaleManager.isLastScale():
s = config.sigBlur[scaleList.index(sc)]
r = config.kerBlur[scaleList.index(sc)]
gausFilt.updateParams(I_tar.size(), ca.Vec3Df(r, r, r),
ca.Vec3Di(s, s, s))
gausFilt.filter(scratchITar, I_tar, temp)
gausFilt.filter(scratchI, I_src, temp)
# ca.Copy(scratchI, I_src)
# ca.Copy(scratchITar, I_tar)
else:
s = config.sigBlur[scaleList.index(sc)]
r = config.kerBlur[scaleList.index(sc)]
gausFilt.updateParams(I_tar.size(), ca.Vec3Df(r, r, r),
ca.Vec3Di(s, s, s))
gausFilt.filter(I_tar_blur, I_tar, temp)
gausFilt.filter(I_src_blur, I_src, temp)
resampler.downsampleImage(scratchI, I_src_blur)
resampler.downsampleImage(scratchITar, I_tar_blur)
if scaleManager.isFirstScale():
scratchF.setGrid(curGrid)
scratchITar.setGrid(curGrid)
ca.SetToIdentity(scratchF)
ca.ApplyH(scratchISrc, scratchI, scratchF)
else:
compF.setGrid(scratchF.grid())
ca.ComposeHH(compF, scratchF, h)
resampler.updateHField(scratchF)
resampler.updateHField(compF)
ca.Copy(scratchF, compF)
ca.ApplyH(scratchISrc, scratchI, compF)
for sc in scaleList:
SetScale(scaleList.index(sc))
#Set the optimize parameters in the IDiff configuration object
idConf.optim.Niter = config.iters[scaleList.index(sc)]
idConf.optim.stepSize = config.epsReg[scaleList.index(sc)]
idConf.idiff.regWeight = config.sigReg[scaleList.index(sc)]
ca.Copy(idConf.study.I0, scratchISrc)
ca.Copy(idConf.study.I1, scratchITar)
idConf.io.plotEvery = config.iters[scaleList.index(sc)]
h = IDiff.Matching.Matching(idConf)
tempScr = scratchISrc.copy()
ca.ApplyH(tempScr, scratchISrc, h)
#Plot the images to see the change
cd.DispImage(scratchISrc - scratchITar,
rng=[-2, 2],
title='Orig Diff',
colorbar=True)
cd.DispImage(tempScr - scratchITar,
rng=[-2, 2],
title='Reg Diff',
colorbar=True)
# common.DebugHere()
# I_src_def = idConf.study.I0.copy()
# scratchITar = idConf.study.I1
# eps = config.epsReg[scaleList.index(sc)]
# sigma = config.sigReg[scaleList.index(sc)]
# nIter = config.iters[scaleList.index(sc)]
# # common.DebugHere()
# [I_src_def, h, energy] = apps.IDiff(scratchISrc, scratchITar, eps, sigma, nIter, plot=True, verbose=1)
ca.ComposeHH(scratchF, compF, h)
I_src_def = idConf.study.I0.copy()
return I_src_def, scratchF
