def volLoad(vlist, cachePath, kssBlurStr, verbose):
kSSblur = teem.nrrdKernelSpecNew()
if (teem.nrrdKernelSpecParse(kSSblur, kssBlurStr)):
estr = teem.biffGetDone('nrrd')
print "problem with kernel:\n%s" % estr
sys.exit(1)
vol = (ctypes.POINTER(teem.meetPullVol) * len(vlist))()
E = 0
for i in range(len(vlist)):
vol[i] = teem.meetPullVolNew()
if (not E):
E += teem.meetPullVolParse(vol[i], vlist[i])
if (not E):
E += teem.meetPullVolLoadMulti(vol, len(vol), cachePath, kSSblur,
teem.nrrdBoundaryWrap, 0.0, verbose)
if (E):
estr = teem.biffGetDone('meet')
print "problem with volumes:\n%s" % estr
sys.exit(1)
teem.nrrdKernelSpecNix(kSSblur)
return vol
def volLoad(vlist, cachePath, kssBlurStr, verbose):
kSSblur = teem.nrrdKernelSpecNew()
if (teem.nrrdKernelSpecParse(kSSblur, kssBlurStr)):
estr = teem.biffGetDone('nrrd')
print "problem with kernel:\n%s" % estr
sys.exit(1)
vol = (ctypes.POINTER(teem.meetPullVol) * len(vlist))()
E = 0
for i in range(len(vlist)):
vol[i] = teem.meetPullVolNew()
if (not E):
E += teem.meetPullVolParse(vol[i], vlist[i])
if (not E):
E += teem.meetPullVolLoadMulti(vol, len(vol),
cachePath, kSSblur, verbose)
if (E):
estr = teem.biffGetDone('meet')
print "problem with volumes:\n%s" % estr
sys.exit(1)
teem.nrrdKernelSpecNix(kSSblur)
return vol
def energyParse(**kwargs):
type = kwargs['type']
if (teem.pullInterTypeJustR == type
or teem.pullInterTypeUnivariate == type):
espec = [teem.pullEnergySpecNew(), None, None]
elif (teem.pullInterTypeSeparable == type):
espec = [teem.pullEnergySpecNew(),
teem.pullEnergySpecNew(), None]
elif (teem.pullInterTypeAdditive == type):
espec = [teem.pullEnergySpecNew(),
teem.pullEnergySpecNew(),
teem.pullEnergySpecNew()]
lett = ['r', 's', 'w']
E = 0
for i in range(3):
if (not E and espec[i]):
E += teem.pullEnergySpecParse(espec[i], kwargs[lett[i]])
if (E):
estr = teem.biffGetDone('pull')
print "problem with infos:\n%s" % estr
sys.exit(1)
ret = [type, espec[0], espec[1], espec[2]]
return ret
import sys
import teem
import pullDemo
import ctypes
npos = teem.nrrdNew()
vol = pullDemo.volLoad(['../../data/fmob-c4h.nrrd:scalar:V'], './', 'ds:1,5', 1)
infoList = ['h-c:V:val:0:-1',
'hgvec:V:gvec',
'hhess:V:hess',
'tan1:V:hevec2',
'strn:V:heval2:0:-1',
'lthr:V:heval2:-70:-1',
'sthr:V:heval2:-70:-1']
pullDemo.run(npos,
init=[teem.pullInitMethodRandom, 300],
efs=False,
vol=vol,
info=infoList,
energy={'type':teem.pullInterTypeJustR, 'r':'cwell:0.6,-0.002'},
iterMax=200,
radSpace=0.05)
pullDemo.volFree(vol)
if (teem.nrrdSave("npos.nrrd", npos, None)):
estr = teem.biffGetDone('nrrd')
print "problem running system:\n%s" % estr
sys.exit(1)
def run(nposOut, **args):
global gamma
if (not ('vol' in args and 'info' in args and 'efs' in args)):
print "run: didn't get vol, info, and efs args"
sys.exit(1)
# learn args, with defaults
vol = a(args, 'vol')
infoStr = a(args, 'info')
efs = a(args, 'efs')
init = a(args, 'init', [teem.pullInitMethodRandom, 100])
energyDict = a(args, 'energy', {'type':teem.pullInterTypeJustR,
'r':'qwell:0.68'})
verbose = a(args, 'verbose', 1)
rngSeed = a(args, 'rngSeed', 42)
nobin = a(args, 'nobin', False)
noadd = a(args, 'noadd', False)
ac3c = a(args, 'ac3c', False)
usa = a(args, 'usa', False)
nave = a(args, 'nave', True)
cbst = a(args, 'cbst', True)
ratb = a(args, 'ratb', True)
lti = a(args, 'lti', False)
npcwza = a(args, 'npcwza', False)
ubfgl = a(args, 'ubfgl', False)
iterMin = a(args, 'iterMin', 0)
iterMax = a(args, 'iterMax', 100)
snap = a(args, 'snap', 0)
pcp = a(args, 'pcp', 5)
iad = a(args, 'iad', 10)
radSpace = a(args, 'radSpace', 1)
radScale = a(args, 'radScale', 1)
alpha = a(args, 'alpha', 0.5)
beta = a(args, 'beta', 0.5)
gamma = a(args, 'gamma', 1)
stepInitial = a(args, 'step', 1)
ssBack = a(args, 'ssBack', 0.2)
ssOppor = a(args, 'ssOppor', 1.1)
pbm = a(args, 'pbm', 50)
k00Str = a(args, 'k00', 'c4h')
k11Str = a(args, 'k11', 'c4hd')
k22Str = a(args, 'k22', 'c4hdd')
kSSreconStr = a(args, 'kSSrecon', 'hermite')
eip = a(args, 'eip', 0.00005)
eiphl = a(args, 'eiphl', 0)
fnnm = a(args, 'fnnm', 0.25)
edmin = a(args, 'edmin', 0.00001)
edpcmin = a(args, 'edpcmin', 0.01)
maxci = a(args, 'maxci', 15)
if args:
print
print "sorry, got unrecognized arguments:"
print args
sys.exit(1)
# create pullContext and set up all its state. Its kind of silly that
# the pullContext is created anew everytime we want to run it, but thats
# because currently the pullContext doesn't have the kind of internal
# network of flags (like the gageContext does) that allow the context
# to be modifyied and re-used indefinitely. This will be fixed after
# the Teem v1.11 release.
pctx = teem.pullContextNew()
energyList = energyParse(**energyDict)
if (teem.pullVerboseSet(pctx, verbose) or
teem.pullRngSeedSet(pctx, rngSeed) or
teem.pullFlagSet(pctx, teem.pullFlagNixAtVolumeEdgeSpace, nave) or
teem.pullFlagSet(pctx, teem.pullFlagConstraintBeforeSeedThresh,
cbst) or
teem.pullFlagSet(pctx, teem.pullFlagEnergyFromStrength, efs) or
teem.pullFlagSet(pctx, teem.pullFlagRestrictiveAddToBins, ratb) or
teem.pullFlagSet(pctx, teem.pullFlagNoPopCntlWithZeroAlpha, npcwza) or
teem.pullFlagSet(pctx, teem.pullFlagUseBetaForGammaLearn, ubfgl) or
teem.pullFlagSet(pctx, teem.pullFlagBinSingle, nobin) or
teem.pullFlagSet(pctx, teem.pullFlagNoAdd, noadd) or
teem.pullFlagSet(pctx,
teem.pullFlagAllowCodimension3Constraints,
ac3c) or
teem.pullInitUnequalShapesAllowSet(pctx, usa) or
teem.pullIterParmSet(pctx, teem.pullIterParmMin, iterMin) or
teem.pullIterParmSet(pctx, teem.pullIterParmMax, iterMax) or
teem.pullIterParmSet(pctx, teem.pullIterParmSnap, snap) or
teem.pullIterParmSet(pctx, teem.pullIterParmConstraintMax, maxci) or
teem.pullIterParmSet(pctx, teem.pullIterParmPopCntlPeriod, pcp) or
teem.pullIterParmSet(pctx, teem.pullIterParmAddDescent, iad) or
teem.pullIterParmSet(pctx,
teem.pullIterParmEnergyIncreasePermitHalfLife,
eiphl) or
teem.pullSysParmSet(pctx, teem.pullSysParmStepInitial, stepInitial) or
teem.pullSysParmSet(pctx, teem.pullSysParmRadiusSpace, radSpace) or
teem.pullSysParmSet(pctx, teem.pullSysParmRadiusScale, radScale) or
teem.pullSysParmSet(pctx, teem.pullSysParmAlpha, alpha) or
teem.pullSysParmSet(pctx, teem.pullSysParmBeta, beta) or
teem.pullSysParmSet(pctx, teem.pullSysParmGamma, gamma) or
teem.pullSysParmSet(pctx, teem.pullSysParmEnergyIncreasePermit, eip) or
teem.pullSysParmSet(pctx, teem.pullSysParmFracNeighNixedMax, fnnm) or
teem.pullSysParmSet(pctx, teem.pullSysParmEnergyDecreaseMin, edmin) or
teem.pullSysParmSet(pctx, teem.pullSysParmEnergyDecreasePopCntlMin,
edpcmin) or
teem.pullSysParmSet(pctx, teem.pullSysParmBackStepScale, ssBack) or
teem.pullSysParmSet(pctx, teem.pullSysParmOpporStepScale, ssOppor) or
teem.pullProgressBinModSet(pctx, pbm) or
teem.pullInterEnergySet(pctx, energyList[0], energyList[1],
energyList[2], energyList[3])):
estr = teem.biffGetDone('pull')
print "problem with set-up:\n%s" % estr
sys.exit(1)
# The meet library offers a slightly higher-level abstraction of
# the pullInfo; this code parses a bunch of info specifications
info = (ctypes.POINTER(teem.meetPullInfo) * len(infoStr))()
for i in range(len(infoStr)):
info[i] = teem.meetPullInfoNew()
if (teem.meetPullInfoParse(info[i], infoStr[i])):
estr = teem.biffGetDone('meet')
print "problem with infos:\n%s" % estr
sys.exit(1)
# Create all the kernels needed for reconstruction
k00 = teem.nrrdKernelSpecNew()
k11 = teem.nrrdKernelSpecNew()
k22 = teem.nrrdKernelSpecNew()
kSSrecon = teem.nrrdKernelSpecNew()
if (teem.nrrdKernelSpecParse(k00, k00Str) or
teem.nrrdKernelSpecParse(k11, k11Str) or
teem.nrrdKernelSpecParse(k22, k22Str) or
teem.nrrdKernelSpecParse(kSSrecon, kSSreconStr)):
estr = teem.biffGetDone('nrrd')
print "problem with kernels:\n%s" % estr
sys.exit(1)
# We do assume that the volumes came in loaded (as opposed to reloading
# them here for every one); here we add all the volumes and infos into
# the pullContext
if (teem.meetPullVolAddMulti(pctx, vol, len(vol),
k00, k11, k22, kSSrecon) or
teem.meetPullInfoAddMulti(pctx, info, len(info))):
estr = teem.biffGetDone('meet')
print "problem with infos:\n%s" % estr
sys.exit(1)
# Final setup and the actual "pullRun" call
if (initSet(pctx, init) or
teem.pullInitLiveThreshUseSet(pctx, lti) or
teem.pullStart(pctx) or
teem.pullRun(pctx) or
teem.pullOutputGet(nposOut, None, None, None, 0, pctx)):
estr = teem.biffGetDone('pull')
print "problem running system:\n%s" % estr
sys.exit(1)
# until there's a clean way to re-use a pullContext for different runs,
# there's no good way for the user to call pullGammaLearn (because pctx
# doesn't survive outside the call to "run". So we call pullGammaLearn
# it whenever it makes sense to do so and save the result in the global
# "gamma"
if (teem.pullInterTypeAdditive == pctx.contents.interType and
teem.pullEnergyButterworthParabola.contents.name
== pctx.contents.energySpecS.contents.energy.contents.name):
if (teem.pullGammaLearn(pctx)):
estr = teem.biffGetDone('pull')
print "problem learning gamma:\n%s" % estr
sys.exit(1)
gamma = pctx.contents.sysParm.gamma
print "pullGammaLearn returned", gamma
teem.nrrdKernelSpecNix(k00)
teem.nrrdKernelSpecNix(k11)
teem.nrrdKernelSpecNix(k22)
teem.nrrdKernelSpecNix(kSSrecon)
energyFree(energyList)
teem.pullContextNix(pctx)
return
import teem
import pullDemo
import ctypes
npos = teem.nrrdNew()
vol = pullDemo.volLoad(['../../data/fmob-c4h.nrrd:scalar:V'], './', 'ds:1,5',
1)
infoList = [
'h-c:V:val:0:-1', 'hgvec:V:gvec', 'hhess:V:hess', 'tan1:V:hevec2',
'strn:V:heval2:0:-1', 'lthr:V:heval2:-70:-1', 'sthr:V:heval2:-70:-1'
]
pullDemo.run(npos,
init=[teem.pullInitMethodRandom, 300],
efs=False,
vol=vol,
info=infoList,
energy={
'type': teem.pullInterTypeJustR,
'r': 'cwell:0.6,-0.002'
},
iterMax=200,
radSpace=0.05)
pullDemo.volFree(vol)
if (teem.nrrdSave("npos.nrrd", npos, None)):
estr = teem.biffGetDone('nrrd')
print "problem running system:\n%s" % estr
sys.exit(1)