def test_GroupAdjointAction(self, disp=False):
hM = common.RandField(self.sz,
nSig=5.0,
gSig=4.0,
mType=ca.MEM_HOST,
sp=self.imSp)
hV = common.RandField(self.sz,
nSig=5.0,
gSig=4.0,
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.Field3D(self.grid, ca.MEM_HOST)
# compute < m, Ad_\phi v >
ca.Ad(tmp, hPhi, hV)
rhs = ca.Dot(tmp, hM)
# compute < Ad^*_\phi m, v >
ca.CoAd(tmp, hPhi, hM)
lhs = ca.Dot(tmp, hV)
#print "a=%f b=%f" % (rhs, lhs)
self.assertLess(abs(rhs - lhs), 2e-6)
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 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
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)