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)
def test_SplatAdjoint(self, disp=False):
hI = common.RandImage(self.sz,
nSig=1.0,
gSig=0.0,
mType=ca.MEM_HOST,
sp=self.imSp)
hJ = common.RandImage(self.sz,
nSig=1.0,
gSig=0.0,
mType=ca.MEM_HOST,
sp=self.imSp)
hPhi = common.RandField(self.sz,
nSig=5.0,
gSig=4.0,
mType=ca.MEM_HOST,
sp=self.imSp)
tmp = ca.Image3D(self.grid, ca.MEM_HOST)
# compute < I(Phi(x)), J(x) >
ca.ApplyH(tmp, hI, hPhi)
phiIdotJ = ca.Dot(tmp, hJ)
# compute < I(y), |DPhi^{-1}(y)| J(Phi^{-1}(y)) >
ca.Splat(tmp, hPhi, hJ)
IdotphiJ = ca.Dot(tmp, hI)
#print "a=%f b=%f" % (phiIdotJ, IdotphiJ)
self.assertLess(abs(phiIdotJ - IdotphiJ), 2e-6)
def geodesic_shooting_diffOp(moving, target, m0, steps, mType, config):
grid = moving.grid()
m0.setGrid(grid)
ca.ThreadMemoryManager.init(grid, mType, 1)
if mType == ca.MEM_HOST:
diffOp = ca.FluidKernelFFTCPU()
else:
diffOp = ca.FluidKernelFFTGPU()
diffOp.setAlpha(config['deformation_params']['diffOpParams'][0])
diffOp.setBeta(config['deformation_params']['diffOpParams'][1])
diffOp.setGamma(config['deformation_params']['diffOpParams'][2])
diffOp.setGrid(grid)
g = ca.Field3D(grid, mType)
ginv = ca.Field3D(grid, mType)
mt = ca.Field3D(grid, mType)
It = ca.Image3D(grid, mType)
It_inv = ca.Image3D(grid, mType)
if (steps <= 0):
time_steps = config['deformation_params']['timeSteps'];
else:
time_steps = steps;
t = [x*1./time_steps for x in range(time_steps+1)]
checkpointinds = range(1,len(t))
checkpointstates = [(ca.Field3D(grid,mType),ca.Field3D(grid,mType)) for idx in checkpointinds]
scratchV1 = ca.Field3D(grid,mType)
scratchV2 = ca.Field3D(grid,mType)
scratchV3 = ca.Field3D(grid,mType)
CAvmCommon.IntegrateGeodesic(m0,t,diffOp, mt, g, ginv,\
scratchV1,scratchV2,scratchV3,\
keepstates=checkpointstates,keepinds=checkpointinds,
Ninv=config['deformation_params']['NIterForInverse'], integMethod = config['deformation_params']['integMethod'])
ca.ApplyH(It,moving,ginv)
ca.ApplyH(It_inv,target,g)
output={'I1':It, 'I1_inv': It_inv, "phiinv":ginv}
return output
def DefSeriesIter(I, V, t, func, args):
grid = I.grid()
mType = I.memType()
tlen = len(t)
h = core.Field3D(grid, mType)
IDef = core.Image3D(grid, mType)
core.SetToIdentity(h)
scratchV1 = core.Field3D(grid, mType)
scratchV2 = core.Field3D(grid, mType)
rtnarr = []
for tidx in range(tlen):
curt = t[tidx]
h = common.ComposeDef(V, curt, inverse=True,
asVField=False,
scratchV1=scratchV1,
scratchV2=scratchV2)
core.ApplyH(IDef, I, h)
r = func(IDef, curt, *args)
rtnarr.append(r)
return rtnarr
def MatchingGradient(p):
# shoot the geodesic forward
CAvmCommon.IntegrateGeodesic(p.m0,p.t,p.diffOp, \
p.m, p.g, p.ginv,\
p.scratchV1, p.scratchV2,p. scratchV3,\
p.checkpointstates, p.checkpointinds,\
Ninv=p.nInv, integMethod = p.integMethod, RK4=p.scratchV4,scratchG=p.scratchV5)
endidx = p.checkpointinds.index(len(p.t)-1)
# compute residual image
ca.ApplyH(p.residualIm,p.I0,p.ginv)
ca.Sub_I(p.residualIm, p.I1)
# while we have residual, save the image energy
IEnergy = ca.Sum2(p.residualIm)/(2*p.sigma*p.sigma*float(p.I0.nVox()))
ca.DivC_I(p.residualIm, p.sigma*p.sigma) # gradient at measurement
# integrate backward
CAvmCommon.IntegrateAdjoints(p.Iadj,p.madj,\
p.I,p.m,p.Iadjtmp, p.madjtmp,p.scratchV1,\
p.scratchV2,p.scratchV3,\
p.I0,p.m0,\
p.t, p.checkpointstates, p.checkpointinds,\
[p.residualIm], [endidx],\
p.diffOp,
p.integMethod, p.nInv, \
scratchV3=p.scratchV7, scratchV4=p.g,scratchV5=p.ginv,scratchV6=p.scratchV8, scratchV7=p.scratchV9, \
scratchV8=p.scratchV10,scratchV9=p.scratchV11,\
RK4=p.scratchV4, scratchG=p.scratchV5, scratchGinv=p.scratchV6)
# compute gradient
ca.Copy(p.scratchV1, p.m0)
p.diffOp.applyInverseOperator(p.scratchV1)
# while we have velocity, save the vector energy
VEnergy = 0.5*ca.Dot(p.m0,p.scratchV1)/float(p.I0.nVox())
ca.Sub_I(p.scratchV1, p.madj)
#p.diffOp.applyOperator(p.scratchV1)
return (p.scratchV1, VEnergy, IEnergy)
def MatchingImageMomentaComputeEnergy(geodesicState, m0, J1, n1):
vecEnergy = 0.0
imageMatchEnergy = 0.0
momentaMatchEnergy = 0.0
grid = geodesicState.J0.grid()
mType = geodesicState.J0.memType()
imdiff = ca.ManagedImage3D(grid, mType)
vecdiff = ca.ManagedField3D(grid, mType)
# image match energy
ca.ApplyH(imdiff, geodesicState.J0, geodesicState.rhoinv)
ca.Sub_I(imdiff, J1)
imageMatchEnergy = 0.5 * ca.Sum2(imdiff) / (
float(geodesicState.p0.nVox()) * geodesicState.Sigma *
geodesicState.Sigma * geodesicState.SigmaIntercept *
geodesicState.SigmaIntercept) # save for use in intercept energy term
# momenta match energy
ca.CoAd(geodesicState.p, geodesicState.rhoinv, m0)
ca.Sub_I(geodesicState.p, n1)
ca.Copy(vecdiff, geodesicState.p) # save for use in slope energy term
geodesicState.diffOp.applyInverseOperator(geodesicState.p)
momentaMatchEnergy = ca.Dot(vecdiff, geodesicState.p) / (
float(geodesicState.p0.nVox()) * geodesicState.SigmaSlope *
geodesicState.SigmaSlope)
# vector energy. p is used as scratch variable
ca.Copy(geodesicState.p, geodesicState.p0)
geodesicState.diffOp.applyInverseOperator(geodesicState.p)
vecEnergy = 0.5 * ca.Dot(geodesicState.p0, geodesicState.p) / (
float(geodesicState.p0.nVox()) * geodesicState.SigmaIntercept *
geodesicState.SigmaIntercept)
return (vecEnergy, imageMatchEnergy, momentaMatchEnergy)
def MatchingImageMomentaWriteOuput(cf, geodesicState, EnergyHistory, m0, n1):
grid = geodesicState.J0.grid()
mType = geodesicState.J0.memType()
# save momenta for the gedoesic
common.SaveITKField(geodesicState.p0, cf.io.outputPrefix + "p0.mhd")
# save matched momenta for the geodesic
if cf.vectormomentum.matchImOnly:
m0 = common.LoadITKField(cf.study.m, mType)
ca.CoAd(geodesicState.p, geodesicState.rhoinv, m0)
common.SaveITKField(geodesicState.p, cf.io.outputPrefix + "m1.mhd")
# momenta match energy
if cf.vectormomentum.matchImOnly:
vecdiff = ca.ManagedField3D(grid, mType)
ca.Sub_I(geodesicState.p, n1)
ca.Copy(vecdiff, geodesicState.p)
geodesicState.diffOp.applyInverseOperator(geodesicState.p)
momentaMatchEnergy = ca.Dot(vecdiff, geodesicState.p) / (
float(geodesicState.p0.nVox()) * geodesicState.SigmaSlope *
geodesicState.SigmaSlope)
# save energy
energyFilename = cf.io.outputPrefix + "testMomentaMatchEnergy.csv"
with open(energyFilename, 'w') as f:
print >> f, momentaMatchEnergy
# save matched image for the geodesic
tempim = ca.ManagedImage3D(grid, mType)
ca.ApplyH(tempim, geodesicState.J0, geodesicState.rhoinv)
common.SaveITKImage(tempim, cf.io.outputPrefix + "I1.mhd")
# save energy
energyFilename = cf.io.outputPrefix + "energy.csv"
MatchingImageMomentaWriteEnergyHistoryToFile(EnergyHistory, energyFilename)
def WarpGradient(p, t, Imsmts, cpinds, cpstates, msmtinds, gradAtMsmts):
# shoot the geodesic forward
CAvmCommon.IntegrateGeodesic(p.m0,t,p.diffOp, \
p.m, p.g, p.ginv,\
p.scratchV1, p.scratchV2,p. scratchV3,\
cpstates, cpinds,\
Ninv=p.nInv, integMethod = p.integMethod, RK4=p.scratchV4,scratchG=p.scratchV5)
IEnergy = 0.0
# compute residuals for each measurement timepoint along with computing energy
for i in range(len(Imsmts)):
if msmtinds[i] != -1:
(g, ginv) = cpstates[msmtinds[i]]
ca.ApplyH(gradAtMsmts[i], p.I0, ginv)
ca.Sub_I(gradAtMsmts[i], Imsmts[i])
# while we have residual, save the image energy
IEnergy += ca.Sum2(
gradAtMsmts[i]) / (2 * p.sigma * p.sigma * float(p.I0.nVox()))
ca.DivC_I(gradAtMsmts[i],
p.sigma * p.sigma) # gradient at measurement
elif msmtinds[i] == -1:
ca.Copy(gradAtMsmts[i], p.I0)
ca.Sub_I(gradAtMsmts[i], Imsmts[i])
# while we have residual, save the image energy
IEnergy += ca.Sum2(
gradAtMsmts[i]) / (2 * p.sigma * p.sigma * float(p.I0.nVox()))
ca.DivC_I(gradAtMsmts[i],
p.sigma * p.sigma) # gradient at measurement
# integrate backward
CAvmCommon.IntegrateAdjoints(p.Iadj,p.madj,\
p.I,p.m,p.Iadjtmp, p.madjtmp,p.scratchV1,\
p.scratchV2,p.scratchV3,\
p.I0,p.m0,\
t, cpstates, cpinds,\
gradAtMsmts,msmtinds,\
p.diffOp,\
p.integMethod, p.nInv, \
scratchV3=p.scratchV7, scratchV4=p.g,scratchV5=p.ginv,scratchV6=p.scratchV8, scratchV7=p.scratchV9, \
scratchV8=p.scratchV10,scratchV9=p.scratchV11,\
RK4=p.scratchV4, scratchG=p.scratchV5, scratchGinv=p.scratchV6,\
scratchI = p.scratchI1)
# compute gradient
ca.Copy(p.scratchV1, p.m0)
p.diffOp.applyInverseOperator(p.scratchV1)
# while we have velocity, save the vector energy
VEnergy = 0.5 * ca.Dot(p.m0, p.scratchV1) / float(p.I0.nVox())
ca.Sub_I(p.scratchV1, p.madj)
#p.diffOp.applyOperator(p.scratchV1)
# compute closed from terms for image update
# p.Iadjtmp and p.I will be used as scratch images
scratchI = p.scratchI1 #reference assigned
imOnes = p.I #reference assigned
ca.SetMem(imOnes, 1.0)
ca.SetMem(p.sumSplatI, 0.0)
ca.SetMem(p.sumJac, 0.0)
#common.DebugHere()
for i in range(len(Imsmts)):
# TODO: check these indexings for cases when timepoint 0
# is not checkpointed
if msmtinds[i] != -1:
(g, ginv) = cpstates[msmtinds[i]]
CAvmCommon.SplatSafe(scratchI, ginv, Imsmts[i])
ca.Add_I(p.sumSplatI, scratchI)
CAvmCommon.SplatSafe(scratchI, ginv, imOnes)
ca.Add_I(p.sumJac, scratchI)
elif msmtinds[i] == -1:
ca.Add_I(p.sumSplatI, Imsmts[i])
ca.Add_I(p.sumJac, imOnes)
return (p.scratchV1, p.sumJac, p.sumSplatI, VEnergy, IEnergy)
def MatchingImageMomentaPlots(cf,
geodesicState,
tDiscGeodesic,
EnergyHistory,
m0,
J1,
n1,
writeOutput=True):
"""
Do some summary plots for MatchingImageMomenta
"""
#ENERGY
fig = plt.figure(1)
plt.clf()
fig.patch.set_facecolor('white')
TE = [row[0] for row in EnergyHistory]
VE = [row[1] for row in EnergyHistory]
IE = [row[2] for row in EnergyHistory]
ME = [row[3] for row in EnergyHistory]
plt.subplot(2, 2, 1)
plt.plot(TE)
plt.title('Total Energy')
plt.hold(False)
plt.subplot(2, 2, 2)
plt.plot(VE)
plt.title('Vector Energy')
plt.hold(False)
plt.subplot(2, 2, 3)
plt.plot(IE)
plt.title('Image Match Energy')
plt.hold(False)
plt.subplot(2, 2, 4)
plt.plot(ME)
plt.title('Momenta Match Energy')
plt.hold(False)
plt.draw()
plt.show()
if cf.io.outputPrefix != None and writeOutput:
plt.savefig(cf.io.outputPrefix + 'energy.pdf')
# GEODESIC INITIAL CONDITIONS and RHO and RHO inv
CAvmHGMCommon.HGMIntegrateGeodesic(geodesicState.p0, geodesicState.s,
geodesicState.diffOp, geodesicState.p,
geodesicState.rho, geodesicState.rhoinv,
tDiscGeodesic, geodesicState.Ninv,
geodesicState.integMethod)
fig = plt.figure(2)
plt.clf()
fig.patch.set_facecolor('white')
plt.subplot(2, 2, 1)
display.DispImage(geodesicState.J0,
'J0',
newFig=False,
sliceIdx=cf.io.plotSlice)
plt.subplot(2, 2, 2)
ca.ApplyH(geodesicState.J, geodesicState.J0, geodesicState.rhoinv)
display.DispImage(geodesicState.J,
'J1',
newFig=False,
sliceIdx=cf.io.plotSlice)
plt.subplot(2, 2, 3)
display.GridPlot(geodesicState.rhoinv,
every=cf.io.quiverEvery,
color='k',
sliceIdx=cf.io.plotSlice,
isVF=False)
plt.axis('equal')
plt.axis('off')
plt.title('rho^{-1}')
plt.subplot(2, 2, 4)
display.GridPlot(geodesicState.rho,
every=cf.io.quiverEvery,
color='k',
sliceIdx=cf.io.plotSlice,
isVF=False)
plt.axis('equal')
plt.axis('off')
plt.title('rho')
if cf.io.outputPrefix != None and writeOutput:
plt.savefig(cf.io.outputPrefix + 'def.pdf')
# MATCHING DIFFERENCE IMAGES
grid = geodesicState.J0.grid()
mType = geodesicState.J0.memType()
imdiff = ca.ManagedImage3D(grid, mType)
# Image matching
ca.Copy(imdiff, geodesicState.J)
ca.Sub_I(imdiff, J1)
fig = plt.figure(3)
plt.clf()
fig.patch.set_facecolor('white')
plt.subplot(1, 3, 1)
display.DispImage(geodesicState.J0,
'Source J0',
newFig=False,
sliceIdx=cf.io.plotSlice)
plt.colorbar()
plt.subplot(1, 3, 2)
display.DispImage(J1, 'Target J1', newFig=False, sliceIdx=cf.io.plotSlice)
plt.colorbar()
plt.subplot(1, 3, 3)
display.DispImage(imdiff,
'rho.J0-J1',
newFig=False,
sliceIdx=cf.io.plotSlice)
plt.colorbar()
if cf.io.outputPrefix != None and writeOutput:
plt.savefig(cf.io.outputPrefix + 'diffImage.pdf')
# Momenta matching
if mType == ca.MEM_DEVICE:
scratchV1 = ca.Field3D(grid, mType)
scratchV2 = ca.Field3D(grid, mType)
scratchV3 = ca.Field3D(grid, mType)
else:
scratchV1 = ca.ManagedField3D(grid, mType)
scratchV2 = ca.ManagedField3D(grid, mType)
scratchV3 = ca.ManagedField3D(grid, mType)
fig = plt.figure(4)
plt.clf()
fig.patch.set_facecolor('white')
ca.Copy(scratchV1, m0)
scratchV1.toType(ca.MEM_HOST)
m0_x, m0_y, m0_z = scratchV1.asnp()
plt.subplot(2, 3, 1)
plt.imshow(np.squeeze(m0_x))
plt.colorbar()
plt.title('X: Source m0 ')
plt.subplot(2, 3, 4)
plt.imshow(np.squeeze(m0_y))
plt.colorbar()
plt.title('Y: Source m0')
ca.Copy(scratchV2, n1)
scratchV2.toType(ca.MEM_HOST)
n1_x, n1_y, n1_z = scratchV2.asnp()
plt.subplot(2, 3, 2)
plt.imshow(np.squeeze(n1_x))
plt.colorbar()
plt.title('X: Target n1')
plt.subplot(2, 3, 5)
plt.imshow(np.squeeze(n1_y))
plt.colorbar()
plt.title('Y: Target n1')
ca.CoAd(scratchV3, geodesicState.rhoinv, m0)
ca.Sub_I(scratchV3, n1)
scratchV3.toType(ca.MEM_HOST)
diff_x, diff_y, diff_z = scratchV3.asnp()
plt.subplot(2, 3, 3)
plt.imshow(np.squeeze(diff_x))
plt.colorbar()
plt.title('X: rho.m0-n1')
plt.subplot(2, 3, 6)
plt.imshow(np.squeeze(diff_y))
plt.colorbar()
plt.title('Y: rho.m0-n1')
if cf.io.outputPrefix != None and writeOutput:
plt.savefig(cf.io.outputPrefix + 'diffMomenta.pdf')
del scratchV1, scratchV2, scratchV3
del imdiff
plt.subplot(2, 3, 2)
display.DispImage(imLargeLinear, 'Linear', newFig=False)
plt.subplot(2, 3, 3)
display.DispImage(imLargeCubic, 'Cubic', newFig=False)
plt.subplot(2, 3, 5)
display.DispImage(imSmall, 'small', newFig=False)
plt.show()
h = common.WavyDef([50, 50],
nWaves=1,
waveAmp=10,
waveDim=0,
mType=ca.MEM_HOST,
deformation=True)
imDefNN = imLargeNN.copy()
ca.ApplyH(imDefNN, imLargeNN, h, ca.BACKGROUND_STRATEGY_CLAMP,
ca.INTERP_NN)
imDefLinear = imLargeNN.copy()
ca.ApplyH(imDefLinear, imLargeNN, h, ca.BACKGROUND_STRATEGY_CLAMP,
ca.INTERP_LINEAR)
imDefCubic = imLargeNN.copy()
ca.ApplyH(imDefCubic, imLargeNN, h, ca.BACKGROUND_STRATEGY_CLAMP,
ca.INTERP_CUBIC)
plt.figure('interp def test')
plt.subplot(2, 3, 1)
display.DispImage(imDefNN, 'NN', newFig=False)
plt.subplot(2, 3, 2)
display.DispImage(imDefLinear, 'Linear', newFig=False)
plt.subplot(2, 3, 3)
display.DispImage(imDefCubic, 'Cubic', newFig=False)
plt.subplot(2, 3, 5)
display.DispImage(imLargeNN, 'orig', newFig=False)
# 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)
BFI_def_RGB = ca.Field3D(grid2D, BFI.memType())
ca.ApplyH(BFI_def_RGB, BFI_color, phi,
ca.BACKGROUND_STRATEGY_PARTIAL_ZERO)
cc.InsertSlice(BFIDef3D_RGB, BFI_def_RGB, sliceIdx)
if SaveVE:
BFI_def_VE = ca.Image3D(grid2D, BFI.memType())
ca.ApplyH(BFI_def_VE, BFI_VE, phi, ca.BACKGROUND_STRATEGY_PARTIAL_ZERO)
cc.InsertSlice(BFIDef3D_VE, BFI_def_VE, sliceIdx)
if SaveBW:
BFI_def_BW = ca.Image3D(grid2D, BFI.memType())
ca.ApplyH(BFI_def_BW, BFI, phi, ca.BACKGROUND_STRATEGY_PARTIAL_ZERO)
cc.InsertSlice(BFIDef3D_BW, BFI_def_BW, sliceIdx)
# Save BFIDef3D
if SaveInBFICoords:
print 'saving blockface in blockface coords...'
if SaveVE:
cc.WriteMHA(BFIDef3D_VE,
def GeodesicShooting(cf):
# prepare output directory
common.Mkdir_p(os.path.dirname(cf.io.outputPrefix))
# Output loaded config
if cf.io.outputPrefix is not None:
cfstr = Config.ConfigToYAML(GeodesicShootingConfigSpec, cf)
with open(cf.io.outputPrefix + "parsedconfig.yaml", "w") as f:
f.write(cfstr)
mType = ca.MEM_DEVICE if cf.useCUDA else ca.MEM_HOST
#common.DebugHere()
I0 = common.LoadITKImage(cf.study.I0, mType)
m0 = common.LoadITKField(cf.study.m0, mType)
grid = I0.grid()
ca.ThreadMemoryManager.init(grid, mType, 1)
# set up diffOp
if mType == ca.MEM_HOST:
diffOp = ca.FluidKernelFFTCPU()
else:
diffOp = ca.FluidKernelFFTGPU()
diffOp.setAlpha(cf.diffOpParams[0])
diffOp.setBeta(cf.diffOpParams[1])
diffOp.setGamma(cf.diffOpParams[2])
diffOp.setGrid(grid)
g = ca.Field3D(grid, mType)
ginv = ca.Field3D(grid, mType)
mt = ca.Field3D(grid, mType)
It = ca.Image3D(grid, mType)
t = [
x * 1. / cf.integration.nTimeSteps
for x in range(cf.integration.nTimeSteps + 1)
]
checkpointinds = range(1, len(t))
checkpointstates = [(ca.Field3D(grid, mType), ca.Field3D(grid, mType))
for idx in checkpointinds]
scratchV1 = ca.Field3D(grid, mType)
scratchV2 = ca.Field3D(grid, mType)
scratchV3 = ca.Field3D(grid, mType)
# scale momenta to shoot
cf.study.scaleMomenta = float(cf.study.scaleMomenta)
if abs(cf.study.scaleMomenta) > 0.000000:
ca.MulC_I(m0, float(cf.study.scaleMomenta))
CAvmCommon.IntegrateGeodesic(m0,t,diffOp, mt, g, ginv,\
scratchV1,scratchV2,scratchV3,\
keepstates=checkpointstates,keepinds=checkpointinds,
Ninv=cf.integration.NIterForInverse, integMethod = cf.integration.integMethod)
else:
ca.Copy(It, I0)
ca.Copy(mt, m0)
ca.SetToIdentity(ginv)
ca.SetToIdentity(g)
# write output
if cf.io.outputPrefix is not None:
# scale back shotmomenta before writing
if abs(cf.study.scaleMomenta) > 0.000000:
ca.ApplyH(It, I0, ginv)
ca.CoAd(mt, ginv, m0)
ca.DivC_I(mt, float(cf.study.scaleMomenta))
common.SaveITKImage(It, cf.io.outputPrefix + "I1.mhd")
common.SaveITKField(mt, cf.io.outputPrefix + "m1.mhd")
common.SaveITKField(ginv, cf.io.outputPrefix + "phiinv.mhd")
common.SaveITKField(g, cf.io.outputPrefix + "phi.mhd")
GeodesicShootingPlots(g, ginv, I0, It, cf)
if cf.io.saveFrames:
SaveFrames(checkpointstates, checkpointinds, I0, It, m0, mt, cf)
def SaveFrames(checkpointstates, checkpointinds, I0, It, m0, mt, cf):
momentathresh = 0.00002
common.Mkdir_p(os.path.dirname(cf.io.outputPrefix) + '/frames/')
image_idx = 0
fig = plt.figure(1, frameon=False)
plt.clf()
display.DispImage(I0,
'',
newFig=False,
cmap='gray',
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice)
plt.draw()
outfilename = cf.io.outputPrefix + '/frames/I' + str(image_idx).zfill(
5) + '.png'
fig.set_size_inches(4, 4)
plt.savefig(outfilename, bbox_inches='tight', pad_inches=0, dpi=100)
fig = plt.figure(2, frameon=False)
plt.clf()
temp = ca.Field3D(I0.grid(), I0.memType())
ca.SetToIdentity(temp)
common.DebugHere()
CAvmCommon.MyGridPlot(temp,
every=cf.io.gridEvery,
color='k',
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice,
isVF=False,
plotBase=False)
#fig.patch.set_alpha(0)
#fig.patch.set_visible(False)
a = fig.gca()
#a.set_frame_on(False)
a.set_xticks([])
a.set_yticks([])
plt.axis('tight')
plt.axis('image')
plt.axis('off')
plt.draw()
fig.set_size_inches(4, 4)
outfilename = cf.io.outputPrefix + '/frames/invdef' + str(image_idx).zfill(
5) + '.png'
plt.savefig(outfilename, bbox_inches='tight', pad_inches=0, dpi=100)
fig = plt.figure(3, frameon=False)
plt.clf()
CAvmCommon.MyGridPlot(temp,
every=cf.io.gridEvery,
color='k',
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice,
isVF=False,
plotBase=False)
#fig.patch.set_alpha(0)
#fig.patch.set_visible(False)
a = fig.gca()
#a.set_frame_on(False)
a.set_xticks([])
a.set_yticks([])
plt.axis('tight')
plt.axis('image')
plt.axis('off')
plt.draw()
fig.set_size_inches(4, 4)
outfilename = cf.io.outputPrefix + '/frames/def' + str(image_idx).zfill(
5) + '.png'
plt.savefig(outfilename, bbox_inches='tight', pad_inches=0, dpi=100)
fig = plt.figure(4, frameon=False)
plt.clf()
display.DispImage(I0,
'',
newFig=False,
cmap='gray',
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice)
plt.hold('True')
CAvmCommon.MyQuiver(m0,
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice,
every=cf.io.quiverEvery,
thresh=momentathresh,
scaleArrows=0.25,
arrowCol='r',
lineWidth=0.5,
width=0.005)
plt.draw()
plt.hold('False')
outfilename = cf.io.outputPrefix + '/frames/m' + str(image_idx).zfill(
5) + '.png'
fig.set_size_inches(4, 4)
plt.savefig(outfilename, bbox_inches='tight', pad_inches=0, dpi=100)
for i in range(len(checkpointinds)):
image_idx = image_idx + 1
ca.ApplyH(It, I0, checkpointstates[i][1])
fig = plt.figure(1, frameon=False)
plt.clf()
display.DispImage(It,
'',
newFig=False,
cmap='gray',
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice)
plt.draw()
outfilename = cf.io.outputPrefix + '/frames/I' + str(image_idx).zfill(
5) + '.png'
fig.set_size_inches(4, 4)
plt.savefig(outfilename, bbox_inches='tight', pad_inches=0, dpi=100)
fig = plt.figure(2, frameon=False)
plt.clf()
CAvmCommon.MyGridPlot(checkpointstates[i][1],
every=cf.io.gridEvery,
color='k',
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice,
isVF=False,
plotBase=False)
#fig.patch.set_alpha(0)
#fig.patch.set_visible(False)
a = fig.gca()
#a.set_frame_on(False)
a.set_xticks([])
a.set_yticks([])
plt.axis('tight')
plt.axis('image')
plt.axis('off')
plt.draw()
outfilename = cf.io.outputPrefix + '/frames/invdef' + str(
image_idx).zfill(5) + '.png'
fig.set_size_inches(4, 4)
plt.savefig(outfilename, bbox_inches='tight', pad_inches=0, dpi=100)
fig = plt.figure(3, frameon=False)
plt.clf()
CAvmCommon.MyGridPlot(checkpointstates[i][0],
every=cf.io.gridEvery,
color='k',
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice,
isVF=False,
plotBase=False)
#fig.patch.set_alpha(0)
#fig.patch.set_visible(False)
a = fig.gca()
#a.set_frame_on(False)
a.set_xticks([])
a.set_yticks([])
plt.axis('tight')
plt.axis('image')
plt.axis('off')
plt.draw()
outfilename = cf.io.outputPrefix + '/frames/def' + str(
image_idx).zfill(5) + '.png'
fig.set_size_inches(4, 4)
plt.savefig(outfilename, bbox_inches='tight', pad_inches=0, dpi=100)
ca.CoAd(mt, checkpointstates[i][1], m0)
fig = plt.figure(4, frameon=False)
plt.clf()
display.DispImage(It,
'',
newFig=False,
cmap='gray',
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice)
plt.hold('True')
CAvmCommon.MyQuiver(mt,
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice,
every=cf.io.quiverEvery,
thresh=momentathresh,
scaleArrows=0.40,
arrowCol='r',
lineWidth=0.5,
width=0.005)
plt.draw()
plt.hold('False')
outfilename = cf.io.outputPrefix + '/frames/m' + str(image_idx).zfill(
5) + '.png'
fig.set_size_inches(4, 4)
plt.savefig(outfilename, bbox_inches='tight', pad_inches=0, dpi=100)
def HGMPlots(cf,
groupState,
tDiscGroup,
residualState,
tDiscResidual,
index_individual,
writeOutput=True):
"""
Do some summary plots for HGM
"""
#ENERGY
fig = plt.figure(1)
plt.clf()
fig.patch.set_facecolor('white')
TE = [sum(x) for x in groupState.EnergyHistory]
VE = [row[0] for row in groupState.EnergyHistory]
IE = [row[1] for row in groupState.EnergyHistory]
SE = [row[2] for row in groupState.EnergyHistory]
TE = TE[1:]
VE = VE[1:]
IE = IE[1:]
SE = SE[1:]
plt.subplot(2, 2, 1)
plt.plot(TE)
plt.title('Total Energy')
plt.hold(False)
plt.subplot(2, 2, 2)
plt.plot(VE)
plt.title('Vector Energy')
plt.hold(False)
plt.subplot(2, 2, 3)
plt.plot(IE)
plt.title('Intercept Energy')
plt.hold(False)
plt.subplot(2, 2, 4)
plt.plot(SE)
plt.title('Slope Energy')
plt.hold(False)
plt.draw()
plt.show()
if cf.io.outputPrefix != None and writeOutput:
plt.savefig(cf.io.outputPrefix + 'energy.pdf')
# GROUP INITIAL CONDITIONS and PSI and PSI inv
# shoot group geodesic forward
CAvmHGMCommon.HGMIntegrateGeodesic(groupState.m0, groupState.t,
groupState.diffOp, groupState.m,
groupState.g, groupState.ginv,
tDiscGroup, groupState.Ninv,
groupState.integMethod)
fig = plt.figure(2)
plt.clf()
fig.patch.set_facecolor('white')
plt.subplot(2, 2, 1)
display.DispImage(groupState.I0,
'I0',
newFig=False,
sliceIdx=cf.io.plotSlice)
plt.subplot(2, 2, 2)
ca.ApplyH(groupState.I, groupState.I0, groupState.ginv)
display.DispImage(groupState.I,
'I1',
newFig=False,
sliceIdx=cf.io.plotSlice)
plt.subplot(2, 2, 3)
display.GridPlot(groupState.ginv,
every=cf.io.quiverEvery,
color='k',
sliceIdx=cf.io.plotSlice,
isVF=False)
plt.axis('equal')
plt.axis('off')
plt.title('psi^{-1}')
plt.subplot(2, 2, 4)
display.GridPlot(groupState.g,
every=cf.io.quiverEvery,
color='k',
sliceIdx=cf.io.plotSlice,
isVF=False)
plt.axis('equal')
plt.axis('off')
plt.title('psi')
if cf.io.outputPrefix != None and writeOutput:
plt.savefig(cf.io.outputPrefix + 'groupdef.pdf')
# RESIDUAL INITIAL CONDITIONS and RHO and RHO inv
ca.ApplyH(groupState.I, groupState.I0, groupState.ginv)
residualState.J0 = groupState.I
residualState.p0 = tDiscGroup[index_individual].p0
CAvmHGMCommon.HGMIntegrateGeodesic(residualState.p0, residualState.s,
residualState.diffOp, residualState.p,
residualState.rho, residualState.rhoinv,
tDiscResidual, residualState.Ninv,
residualState.integMethod)
fig = plt.figure(3)
plt.clf()
fig.patch.set_facecolor('white')
plt.subplot(2, 2, 1)
display.DispImage(residualState.J0,
'J0',
newFig=False,
sliceIdx=cf.io.plotSlice)
plt.subplot(2, 2, 2)
ca.ApplyH(residualState.J, residualState.J0, residualState.rhoinv)
display.DispImage(residualState.J,
'J1',
newFig=False,
sliceIdx=cf.io.plotSlice)
plt.subplot(2, 2, 3)
display.GridPlot(residualState.rhoinv,
every=cf.io.quiverEvery,
color='k',
sliceIdx=cf.io.plotSlice,
isVF=False)
plt.axis('equal')
plt.axis('off')
plt.title('rho^{-1}')
plt.subplot(2, 2, 4)
display.GridPlot(residualState.rho,
every=cf.io.quiverEvery,
color='k',
sliceIdx=cf.io.plotSlice,
isVF=False)
plt.axis('equal')
plt.axis('off')
plt.title('rho')
if cf.io.outputPrefix != None and writeOutput:
plt.savefig(cf.io.outputPrefix + 'resdef.pdf')
# MATCHING DIFFERENCE IMAGES
grid = groupState.I0.grid()
mType = groupState.I0.memType()
imdiff = ca.ManagedImage3D(grid, mType)
vecdiff = ca.ManagedField3D(grid, mType)
# Intercept matching
ca.Copy(imdiff, residualState.J)
ca.Sub_I(imdiff, tDiscGroup[index_individual].J)
fig = plt.figure(4)
plt.clf()
fig.patch.set_facecolor('white')
plt.subplot(1, 3, 1)
display.DispImage(residualState.J0,
'Source J0',
newFig=False,
sliceIdx=cf.io.plotSlice)
plt.colorbar()
plt.subplot(1, 3, 2)
display.DispImage(tDiscGroup[index_individual].J,
'Target J1',
newFig=False,
sliceIdx=cf.io.plotSlice)
plt.colorbar()
plt.subplot(1, 3, 3)
display.DispImage(imdiff,
'rho.J0-J1',
newFig=False,
sliceIdx=cf.io.plotSlice)
plt.colorbar()
if cf.io.outputPrefix != None and writeOutput:
plt.savefig(cf.io.outputPrefix + 'diffintercept.pdf')
# Slope matching
'''
ca.CoAd(groupState.m,groupState.ginv,groupState.m0)
ca.CoAd(vecdiff,residualState.rhoinv,groupState.m)
n0 = ca.Field3D(grid, ca.MEM_HOST)
n1 = ca.Field3D(grid, ca.MEM_HOST)
ca.Copy(n0,groupState.m)
ca.Copy(n1,tDiscGroup[index_individual].n)
ca.Sub_I(vecdiff, tDiscGroup[index_individual].n)
vecdiff.toType(ca.MEM_HOST)
n0_x, n0_y, n0_z = n0.asnp()
n1_x, n1_y, n1_z = n1.asnp()
diff_x, diff_y, diff_z = vecdiff.asnp()
fig = plt.figure(5)
plt.clf()
fig.patch.set_facecolor('white')
plt.subplot(2,3,1)
plt.imshow(np.squeeze(n0_x)); plt.colorbar(); plt.title('X: Source n0 ')
plt.subplot(2,3,2)
plt.imshow(np.squeeze(n1_x)); plt.colorbar(); plt.title('X: Target n1')
plt.subplot(2,3,3)
plt.imshow(np.squeeze(diff_x)); plt.colorbar(); plt.title('X: rho.n0-n1')
plt.subplot(2,3,4)
plt.imshow(np.squeeze(n0_y)); plt.colorbar(); plt.title('Y: Source n0')
plt.subplot(2,3,5)
plt.imshow(np.squeeze(n1_y)); plt.colorbar(); plt.title('Y: Target n1')
plt.subplot(2,3,6)
plt.imshow(np.squeeze(diff_y)); plt.colorbar(); plt.title('Y: rho.n0-n1')
if cf.io.outputPrefix != None and writeOutput: plt.savefig(cf.io.outputPrefix+'diffslope.pdf')
'''
del imdiff
del vecdiff
def MatchingPlots(p):
"""
Do some summary plots for image matching
"""
#reset all variables by shooting once, may have been overwritten
CAvmCommon.IntegrateGeodesic(p.m0,p.t,p.diffOp,\
p.m, p.g, p.ginv,\
p.scratchV1, p.scratchV2,p. scratchV3,\
p.checkpointstates, p.checkpointinds,\
Ninv=p.nInv, integMethod = p.integMethod)
# plot the images
fig = plt.figure('images')
plt.clf()
fig.patch.set_facecolor('white')
plt.subplot(2, 2, 1)
display.DispImage(p.I0,
'I0',
newFig=False,
cmap='gray',
sliceIdx=p.plotSlice)
plt.subplot(2, 2, 2)
indx_of_last_tp = p.checkpointinds.index(len(p.t) - 1)
(g, ginv) = p.checkpointstates[indx_of_last_tp]
ca.ApplyH(p.I, p.I0, ginv)
display.DispImage(p.I,
'\phi.I0',
newFig=False,
cmap='gray',
sliceIdx=p.plotSlice)
plt.subplot(2, 2, 3)
display.DispImage(p.I1,
'I1',
newFig=False,
cmap='gray',
sliceIdx=p.plotSlice)
plt.subplot(2, 2, 4)
ca.ApplyH(p.I, p.I1, g)
display.DispImage(p.I,
'\phi^{-1}.I1',
newFig=False,
cmap='gray',
sliceIdx=p.plotSlice)
plt.draw()
plt.show()
if p.outputPrefix != None: plt.savefig(p.outputPrefix + 'images.pdf')
fig = plt.figure('def')
plt.clf()
fig.patch.set_facecolor('white')
plt.subplot(2, 2, 1)
display.GridPlot(ginv,
every=p.quiverEvery,
color='k',
sliceIdx=p.plotSlice,
isVF=False)
plt.axis('equal')
plt.axis('off')
plt.title('\phi^{-1}')
plt.subplot(2, 2, 2)
display.GridPlot(g,
every=p.quiverEvery,
color='k',
sliceIdx=p.plotSlice,
isVF=False)
plt.axis('equal')
plt.axis('off')
plt.title('\phi')
plt.subplot(2, 2, 3)
ca.JacDetH(p.I, ginv) #p.I used as scratch variable to compute jacobian
display.DispImage(p.I, '|D\phi^{-1}|', newFig=False, sliceIdx=p.plotSlice)
plt.subplot(2, 2, 4)
ca.MulC_I(p.residualIm, p.sigma * p.sigma)
display.DispImage(p.residualIm,
'\phi.I0-I1',
newFig=False,
sliceIdx=p.plotSlice)
plt.colorbar()
plt.draw()
plt.show()
if p.outputPrefix != None: plt.savefig(p.outputPrefix + 'def.pdf')
fig = plt.figure('energy')
fig.patch.set_facecolor('white')
TE = [sum(x) for x in p.Energy]
VE = [row[0] for row in p.Energy]
IE = [row[1] for row in p.Energy]
plt.subplot(1, 3, 1)
plt.plot(TE)
plt.title('Total Energy')
plt.hold(False)
plt.subplot(1, 3, 2)
plt.plot(VE)
plt.title('Vector Energy')
plt.hold(False)
plt.subplot(1, 3, 3)
plt.plot(IE)
plt.title('Image Energy')
plt.hold(False)
plt.draw()
plt.show()
if p.outputPrefix != None: plt.savefig(p.outputPrefix + 'energy.pdf')
def ApplyAffine(Iout, Im, A, bg=ca.BACKGROUND_STRATEGY_PARTIAL_ZERO):
'''Applies an Affine matrix A to an image Im using the Image3D
grid (size, spacing, origin) of the two images (Input and Output)
'''
# algorithm outline: Create a temporary large grid, then perform
# real affine transforms here, then crop to be the size of the out grid
ca.SetMem(Iout, 0.0)
A = np.matrix(A)
bigsize = [max(Iout.grid().size().x, Im.grid().size().x),
max(Iout.grid().size().y, Im.grid().size().y),
max(Iout.grid().size().z, Im.grid().size().z)]
idgrid = ca.GridInfo(ca.Vec3Di(bigsize[0], bigsize[1], bigsize[2]),
ca.Vec3Df(1, 1, 1),
ca.Vec3Df(0, 0, 0))
# newgrid = Iout.grid() # not a true copy!!!!!
newgrid = ca.GridInfo(Iout.grid().size(),
Iout.grid().spacing(),
Iout.grid().origin())
mType = Iout.memType()
Imbig = cc.PadImage(Im, bigsize)
h = ca.Field3D(idgrid, mType)
ca.SetToIdentity(h)
if isinstance(Im, ca.Field3D):
Ioutbig = ca.Field3D(idgrid, mType)
else:
Ioutbig = ca.Image3D(idgrid, mType)
# note: x_real' = A*x_real; x_real' given (input grid)
# solution: x_real = A^-1 * x_real
# where x_real = x_index*spacing + origin
# and x_real' = x_index'*spacing' + origin'
# x_index' is really given, as is both spacings/origins
# and we plug in the solution for x_index' into applyH
if A.shape[1] == 3: # 2D affine matrix
x = ca.Image3D(idgrid, mType)
y = ca.Image3D(idgrid, mType)
xnew = ca.Image3D(idgrid, mType)
ynew = ca.Image3D(idgrid, mType)
ca.Copy(x, h, 0)
ca.Copy(y, h, 1)
# convert x,y to world coordinates
x *= Iout.grid().spacing().x
y *= Iout.grid().spacing().y
x += Iout.grid().origin().x
y += Iout.grid().origin().y
# Matrix Multiply (All in real coords)
Ainv = A.I
ca.MulC_Add_MulC(xnew, x, Ainv[0, 0], y, Ainv[0, 1])
ca.MulC_Add_MulC(ynew, x, Ainv[1, 0], y, Ainv[1, 1])
xnew += (Ainv[0, 2])
ynew += (Ainv[1, 2]) # xnew and ynew are now in real coords
# convert back to index coordinates
xnew -= Im.grid().origin().x
ynew -= Im.grid().origin().y
xnew /= Im.grid().spacing().x
ynew /= Im.grid().spacing().y
ca.SetToZero(h)
ca.Copy(h, xnew, 0)
ca.Copy(h, ynew, 1)
elif A.shape[1] == 4: # 3D affine matrix
x = ca.Image3D(idgrid, mType)
y = ca.Image3D(idgrid, mType)
z = ca.Image3D(idgrid, mType)
xnew = ca.Image3D(idgrid, mType)
ynew = ca.Image3D(idgrid, mType)
znew = ca.Image3D(idgrid, mType)
ca.Copy(x, h, 0)
ca.Copy(y, h, 1)
ca.Copy(z, h, 2)
x *= Iout.grid().spacing().x
y *= Iout.grid().spacing().y
z *= Iout.grid().spacing().z
x += Iout.grid().origin().x
y += Iout.grid().origin().y
z += Iout.grid().origin().z
# Matrix Multiply (All in real coords)
Ainv = A.I
ca.MulC_Add_MulC(xnew, x, Ainv[0, 0], y, Ainv[0, 1])
ca.Add_MulC_I(xnew, z, Ainv[0, 2])
xnew += (Ainv[0, 3])
ca.MulC_Add_MulC(ynew, x, Ainv[1, 0], y, Ainv[1, 1])
ca.Add_MulC_I(ynew, z, Ainv[1, 2])
ynew += (Ainv[1, 3])
ca.MulC_Add_MulC(znew, x, Ainv[2, 0], y, Ainv[2, 1])
ca.Add_MulC_I(znew, z, Ainv[2, 2])
znew += (Ainv[2, 3])
# convert to index coordinates
xnew -= Im.grid().origin().x
ynew -= Im.grid().origin().y
znew -= Im.grid().origin().z
xnew /= Im.grid().spacing().x
ynew /= Im.grid().spacing().y
znew /= Im.grid().spacing().z
ca.Copy(h, xnew, 0)
ca.Copy(h, ynew, 1)
ca.Copy(h, znew, 2)
Imbig.setGrid(idgrid)
ca.ApplyH(Ioutbig, Imbig, h, bg)
# crop Ioutbig -> Iout
ca.SubVol(Iout, Ioutbig, ca.Vec3Di(0, 0, 0))
Iout.setGrid(newgrid) # change back
def Matching(cf):
if cf.compute.useCUDA and cf.compute.gpuID is not None:
ca.SetCUDADevice(cf.compute.gpuID)
if os.path.isfile(cf.io.outputPrefix + 'm0.mhd'):
print cf.io.outputPrefix
return ()
# if os.path.isfile(cf.io.outputPrefix+'m0.mhd'):
# return();
# else:
# print cf.io.outputPrefix;
# return();
# prepare output directory
common.Mkdir_p(os.path.dirname(cf.io.outputPrefix))
# Output loaded config
if cf.io.outputPrefix is not None:
cfstr = Config.ConfigToYAML(MatchingConfigSpec, cf)
with open(cf.io.outputPrefix + "parsedconfig.yaml", "w") as f:
f.write(cfstr)
mType = ca.MEM_DEVICE if cf.compute.useCUDA else ca.MEM_HOST
I0 = common.LoadITKImage(cf.study.I0, mType)
I1 = common.LoadITKImage(cf.study.I1, mType)
#ca.DivC_I(I0,255.0)
#ca.DivC_I(I1,255.0)
grid = I0.grid()
It = ca.Image3D(grid, mType)
ca.ThreadMemoryManager.init(grid, mType, 1)
#common.DebugHere()
# TODO: need to work on these
t = [x * 1. / cf.optim.nTimeSteps for x in range(cf.optim.nTimeSteps + 1)]
checkpointinds = range(1, len(t))
checkpointstates = [(ca.Field3D(grid, mType), ca.Field3D(grid, mType))
for idx in checkpointinds]
p = MatchingVariables(I0,
I1,
cf.vectormomentum.sigma,
t,
checkpointinds,
checkpointstates,
cf.vectormomentum.diffOpParams[0],
cf.vectormomentum.diffOpParams[1],
cf.vectormomentum.diffOpParams[2],
cf.optim.Niter,
cf.optim.stepSize,
cf.optim.maxPert,
cf.optim.nTimeSteps,
integMethod=cf.optim.integMethod,
optMethod=cf.optim.method,
nInv=cf.optim.NIterForInverse,
plotEvery=cf.io.plotEvery,
plotSlice=cf.io.plotSlice,
quiverEvery=cf.io.quiverEvery,
outputPrefix=cf.io.outputPrefix)
print(p.stepSize)
RunMatching(p)
# write output
if cf.io.outputPrefix is not None:
# reset all variables by shooting once, may have been overwritten
CAvmCommon.IntegrateGeodesic(p.m0,p.t,p.diffOp,\
p.m, p.g, p.ginv,\
p.scratchV1, p.scratchV2,p. scratchV3,\
p.checkpointstates, p.checkpointinds,\
Ninv=p.nInv, integMethod = p.integMethod)
ca.ApplyH(It, I0, p.ginv)
common.SaveITKField(p.m0, cf.io.outputPrefix + "m0.mhd")
common.SaveITKField(p.ginv, cf.io.outputPrefix + "phiinv.mhd")
#common.SaveITKField(p.g, cf.io.outputPrefix+"phi.mhd")
common.SaveITKImage(It, cf.io.outputPrefix + "I1.mhd")
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