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")
# end if
# end Matching
if __name__ == '__main__':
try:
usercfg = Config.Load(spec=MatchingConfigSpec, argv=sys.argv)
except Config.MissingConfigError:
# Don't freak out, this should have printed a sample config to STDOUT
sys.exit(1)
Matching(usercfg)
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 cf.io.outputPrefix != None:
energyFilename = cf.io.outputPrefix + "Energy.pdf"
plt.savefig(energyFilename)
# end AtlasPlots
if __name__ == '__main__':
#common.DebugHere()
try:
usercfg = Config.Load(spec=AtlasConfigSpec, argv=sys.argv)
except Config.MissingConfigError:
# Don't freak out, this should have printed a sample config to STDOUT
sys.exit(1)
Compute.Compute(BuildAtlas, usercfg)
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
# end MatchingImageMomentalots
if __name__ == '__main__':
#common.DebugHere()
try:
usercfg = Config.Load(spec=MatchingImageMomentaConfigSpec,
argv=sys.argv)
except Config.MissingConfigError:
# Don't freak out, this should have printed a sample config to STDOUT
sys.exit(1)
Compute.Compute(MatchingImageMomenta, usercfg)
plt.axis('off')
plt.title('\phi^{-1}')
plt.subplot(2, 2, 3)
display.DispImage(I0,
'I0',
newFig=False,
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice)
plt.subplot(2, 2, 4)
display.DispImage(It,
'I1',
newFig=False,
dim=cf.io.plotSliceDim,
sliceIdx=cf.io.plotSlice)
plt.draw()
plt.show()
if cf.io.outputPrefix != None:
plt.savefig(cf.io.outputPrefix + 'shooting.pdf')
if __name__ == '__main__':
try:
usercfg = Config.Load(spec=GeodesicShootingConfigSpec, argv=sys.argv)
except Config.MissingConfigError:
# Don't freak out, this should have printed a sample config to STDOUT
sys.exit(1)
GeodesicShooting(usercfg)
break
if not foundSub: # need to insert a timepoint for this subject
t.append(subjectsTimeArray[i])
t.sort()
# now create the subject index array
for i in range(numSubjects):
for j in range(len(t)):
if subjectsTimeArray[i] < (
t[j] + epsilon) and subjectsTimeArray[i] > (
t[j] - epsilon): # matches update Sind
Sind[i] = j
break
cpinds = range(1, len(t))
return (t, Sind, cpinds)
# end HGMSetUpCheckpointing
if __name__ == '__main__':
#common.DebugHere()
try:
usercfg = Config.Load(spec=HGMConfigSpec, argv=sys.argv)
except Config.MissingConfigError:
# Don't freak out, this should have printed a sample config to STDOUT
sys.exit(1)
Compute.Compute(BuildHGM, usercfg)
subjectsTimes.append(singleSubjectTimes)
return (subjectsIds, subjectsImagePaths, subjectsTimes)
# end GeoRegLoadSubjectsDetails
def GeoRegLoadSubjectsInitializations(filename):
subjectsInitialImages = []
subjectsInitialMomenta = []
with open(filename, "r") as f:
for line1, line2 in itertools.izip_longest(*[f] * 2):
singleSubjectsInitialImage = line1.rstrip()
subjectsInitialImages.append(singleSubjectsInitialImage)
singleSubjectsInitialMomentum = line2.rstrip()
subjectsInitialMomenta.append(singleSubjectsInitialMomentum)
return (subjectsInitialImages, subjectsInitialMomenta)
# end GeoRegLoadSubjectsInitializations
if __name__ == '__main__':
try:
usercfg = Config.Load(spec=GeoRegConfigSpec, argv=sys.argv)
except Config.MissingConfigError:
# Don't freak out, this should have printed a sample config to STDOUT
sys.exit(1)
Compute.Compute(BuildGeoReg, usercfg)