def fromNDArray(self, array):
if self.base_ref != None:
self.base_ref = None
teem.nrrdNix(self._ctypesobj)
self._ctypesobj = teem.nrrdNew()
try:
cTy, teemTy = ndarrayGetTypes(array)
except Exception as err:
print err
return
c_type_p = ctypes.POINTER(cTy)
if (array.flags.f_contiguous): # memory shared with array
array_p = array.ctypes.data_as(c_type_p)
dims = list(array.shape)
sizes = (ctypes.c_size_t * teem.NRRD_DIM_MAX)(*dims)
teem.nrrdWrap_nva(self._ctypesobj, array_p, teemTy,
ctypes.c_uint(array.ndim), sizes)
self.base_ref = array
elif (array.flags.c_contiguous): # memory shared with array
array_p = array.ctypes.data_as(c_type_p)
dims = list(reversed(array.shape))
sizes = (ctypes.c_size_t * teem.NRRD_DIM_MAX)(*dims)
teem.nrrdWrap_nva(self._ctypesobj, array_p, teemTy,
ctypes.c_uint(array.ndim), sizes)
self.base_ref = array
else: # must make c_contiguous -- memory not shared with array, transfer full control to teem
arr = numpy.ascontiguousarray(array, dtype=array.dtype.type)
array_p = arr.ctypes.data_as(c_type_p)
dims = list(reversed(arr.shape))
nrrd_tmp = teem.nrrdNew()
sizes = (ctypes.c_size_t * teem.NRRD_DIM_MAX)(*dims)
teem.nrrdWrap_nva(nrrd_tmp, array_p, teemTy,
ctypes.c_uint(array.ndim), sizes)
teem.nrrdCopy(self._ctypesobj,
nrrd_tmp) # this call hangs with fmob-ch4.nrrd
teem.nrrdNix(nrrd_tmp)
self.base_ref = None
self._init = True
if isinstance(array, ExtendedArray):
if not array.base_ref is None: # means there is some Nrrd file sharing it's memory with the array
teem.nrrdAxisInfoCopy(self._ctypesobj,
array.base_ref._ctypesobj, None,
teem.NRRD_AXIS_INFO_SIZE_BIT)
def load(self, file, args=None):
if self.base_ref != None:
self.base_ref = None
teem.nrrdNix(self._ctypesobj)
self._ctypesobj = teem.nrrdNew()
teem.nrrdLoad(self._ctypesobj, file, args)
self.base_ref = None
self._init = True
def load(self, file, args=None):
if self.base_ref != None:
self.base_ref = None
teem.nrrdNix(self._ctypesobj)
self._ctypesobj = teem.nrrdNew()
teem.nrrdLoad(self._ctypesobj, file, args)
self.base_ref = None
self._init = True
def fromNDArray(self, array):
if self.base_ref != None:
self.base_ref = None
teem.nrrdNix(self._ctypesobj)
self._ctypesobj = teem.nrrdNew()
try:
cTy, teemTy = ndarrayGetTypes(array)
except Exception as err:
print err
return
c_type_p = ctypes.POINTER(cTy)
if array.flags.f_contiguous: # memory shared with array
array_p = array.ctypes.data_as(c_type_p)
dims = list(array.shape)
sizes = (ctypes.c_size_t * teem.NRRD_DIM_MAX)(*dims)
teem.nrrdWrap_nva(self._ctypesobj, array_p, teemTy, ctypes.c_uint(array.ndim), sizes)
self.base_ref = array
elif array.flags.c_contiguous: # memory shared with array
array_p = array.ctypes.data_as(c_type_p)
dims = list(reversed(array.shape))
sizes = (ctypes.c_size_t * teem.NRRD_DIM_MAX)(*dims)
teem.nrrdWrap_nva(self._ctypesobj, array_p, teemTy, ctypes.c_uint(array.ndim), sizes)
self.base_ref = array
else: # must make c_contiguous -- memory not shared with array, transfer full control to teem
arr = numpy.ascontiguousarray(array, dtype=array.dtype.type)
array_p = arr.ctypes.data_as(c_type_p)
dims = list(reversed(arr.shape))
nrrd_tmp = teem.nrrdNew()
sizes = (ctypes.c_size_t * teem.NRRD_DIM_MAX)(*dims)
teem.nrrdWrap_nva(nrrd_tmp, array_p, teemTy, ctypes.c_uint(array.ndim), sizes)
teem.nrrdCopy(self._ctypesobj, nrrd_tmp) # this call hangs with fmob-ch4.nrrd
teem.nrrdNix(nrrd_tmp)
self.base_ref = None
self._init = True
if isinstance(array, ExtendedArray):
if not array.base_ref is None: # means there is some Nrrd file sharing it's memory with the array
teem.nrrdAxisInfoCopy(self._ctypesobj, array.base_ref._ctypesobj, None, teem.NRRD_AXIS_INFO_SIZE_BIT)
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 __init__(self):
self._ctypesobj = teem.nrrdNew()
# self._init = False
self.base_ref = None
self.teem = teem # world's ugliest hack -- but it appears to work
def __init__(self):
self._ctypesobj = teem.nrrdNew()
# self._init = False
self.base_ref = None
self.teem = teem # world's ugliest hack -- but it appears to work
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)
