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)
Idef, phi0 = IDiff(BFI_VE_def,
MRI_VE,
step=step,
sigma=sigma,
nIters=nIters,
plot=debug,
verbose=1)[:2]
if debug:
time.sleep(3)
plt.close('all')
phi = phi0.copy()
hA = phi0.copy()
cc.AtoH(hA, A) # convert A to h field
ca.ComposeHH(phi, hA, phi0)
# convert grid back
hA.setGrid(grid_orig)
phi0.setGrid(grid_orig)
phi.setGrid(grid_orig)
Idef.setGrid(grid_orig)
BFI_VE.setGrid(grid_orig)
MRI_VE.setGrid(grid_orig)
# Insert Slice back into Volume
if SaveRGB:
BFI_color = common.ExtractSliceVF(BFI_color3D, sliceIdx)
BFI_color.toType(ca.MEM_DEVICE)
BFI_color.setGrid(grid2D)
Ieps,
Isigma,
InIter,
plot=False,
verbose=1)
Idiff = T2_VE - live_VEfilt_ID
cd.Disp3Pane(Idiff, rng=[-3, 3], sliceIdx=dispslice)
cd.EnergyPlot(Ienergy, legend=['Reg', 'Data', 'Total'])
cd.DispHGrid(Iphi)
print ca.MinMax(Iphi)
# Compose the deformations and apply the total deformation to the initial live volume
# tempDef = ca.Field3D(phi.grid(), memT)
totDef = ca.Field3D(phi.grid(), memT)
ca.ComposeHH(totDef, phi, Iphi, ca.BACKGROUND_STRATEGY_CLAMP)
# ca.ComposeHH(totDef, h, tempDef, ca.BACKGROUND_STRATEGY_CLAMP)
#Apply the deformation to the TPS live volume and rotate to the original volume
live_T2reg_rot = T2.copy()
cc.HtoReal(totDef)
cc.ApplyHReal(live_T2reg_rot, liveDef, totDef)
cd.Disp3Pane(live_T2reg_rot)
# live_T2reg = T2.copy()
# cc.ApplyAffineReal(live_T2reg,live_T2reg_rot,np.linalg.inv(rotMat))
# cd.Disp3Pane(live_T2reg)
if write:
cc.WriteMHA(live_T2reg_rot,
SaveDir + 'M13_01_live_as_MRI_full_bw_256_roty-119_flipy.mha')
cc.WriteMHA(live_T2reg, SaveDir + 'M13_01_live_as_MRI_full_bw_256.mha')
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
nIter_I = 200
[def_ID, theta, energy] = apps.IDiff(def_TPS,
M13_aff,
eps,
sigma_I,
nIter_I,
plot=True,
verbose=1)
if write:
cc.WriteMHA(def_ID, M15dir + 'IDiff/M15_01_ID_to_M13.mha')
cc.WriteMHA(theta, M15dir + 'IDiff/M15_01_ID_Field_to_M13.mha')
h = cc.LoadMHA(M15dir + 'TPS/M15_01_TPS_Field_to_M13.mha', memT)
compDef = ca.Field3D(M13_aff.grid(), memT)
ca.ComposeHH(compDef, h, theta, bg=ca.BACKGROUND_STRATEGY_CLAMP)
common.DebugHere()
Final_aff = ca.Image3D(M13_aff.grid(), memT)
cc.ApplyAffineReal(Final_aff, M15, np.linalg.inv(aff))
Final = ca.Image3D(M13_aff.grid(), memT)
cc.ApplyHReal(Final, Final_aff, compDef)
if write:
cc.WriteMHA(Final, M15dir + 'FullDef/M15_01_MRI_as_M13.mha')
cc.WriteMHA(compDef, M15dir + 'FullDef/M15_01_Field_to_M13.mha')
if not M15_to_M13:
write = True
