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#!/usr/bin/env python
##
## Nrrd.py: bridge between Nrrd and Numpy arrays
## Copyright (C) 2013, 2012, 2011, 2010, 2009 University of Chicago
## created by Sam Quinan - samquinan@cs.uchicago.edu
##
## Permission is hereby granted, free of charge, to any person obtaining
## a copy of this software and associated documentation files (the
## "Software"), to deal in the Software without restriction, including
## without limitation the rights to use, copy, modify, merge, publish,
## distribute, sublicense, and/or sell copies of the Software, and to
## permit persons to whom the Software is furnished to do so, subject to
## the following conditions:
##
## The above copyright notice and this permission notice shall be
## included in all copies or substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
## EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
## MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
## NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
## LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
## OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
## WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
##
import numpy, teem, ctypes
# translates from numpy type to teem type
def ndarrayGetTypes( array ):
typeTable = {
numpy.int8 : (ctypes.c_byte, teem.nrrdTypeChar),
numpy.uint8 : (ctypes.c_ubyte, teem.nrrdTypeUChar),
numpy.int16 : (ctypes.c_short, teem.nrrdTypeShort),
numpy.uint16 : (ctypes.c_ushort, teem.nrrdTypeUShort),
numpy.int : (ctypes.c_int, teem.nrrdTypeInt),
numpy.uint : (ctypes.c_uint, teem.nrrdTypeUInt),
numpy.int32 : (ctypes.c_int32, teem.nrrdTypeInt),
numpy.uint32 : (ctypes.c_uint32, teem.nrrdTypeUInt),
numpy.int64 : (ctypes.c_int64, teem.nrrdTypeLLong),
numpy.uint64 : (ctypes.c_uint64, teem.nrrdTypeULLong),
numpy.float : (ctypes.c_float, teem.nrrdTypeFloat),
numpy.double : (ctypes.c_double, teem.nrrdTypeDouble) }
dt = array.dtype.type
if dt not in typeTable:
raise Exception("array type %s not supported" % dt)
# sanity checking
ct, tt = typeTable[dt]
x = numpy.dtype(dt).itemsize
y = ctypes.sizeof(ct)
z = teem.nrrdTypeSize[tt]
if not (x == y) or not (x == z) or not (y == z):
raise Exception("corresponding numpy, teem, and ctypes types are not of the same size")
return typeTable[dt]
def teemTypeToNumpyType(teem_type):
numpy_endianess_glyph = '<' if teem.airMyEndian() == 1234 else '>'
numpy_type_map = {
teem.nrrdTypeChar: numpy_endianess_glyph + 'i1',
teem.nrrdTypeUChar: numpy_endianess_glyph + 'u1',
teem.nrrdTypeShort: numpy_endianess_glyph + 'i2',
teem.nrrdTypeUShort: numpy_endianess_glyph + 'u2',
teem.nrrdTypeInt: numpy_endianess_glyph + 'i4',
teem.nrrdTypeUInt: numpy_endianess_glyph + 'u4',
teem.nrrdTypeLLong: numpy_endianess_glyph + 'i8',
teem.nrrdTypeULLong: numpy_endianess_glyph + 'u8',
teem.nrrdTypeFloat: numpy_endianess_glyph + 'f4',
teem.nrrdTypeDouble: numpy_endianess_glyph + 'f8'
}
return numpy_type_map[teem_type]
# design based on a combination of work done by Carlos Scheidegger
# [ http://code.google.com/p/python-teem/source/browse/trunk/teem/capi/numpy/__init__.py ,
# http://code.google.com/p/python-teem/source/browse/trunk/teem/nrrd.py ]
# and ideas presented by Travis Oliphant [ http://blog.enthought.com/?p=62 ]
class Nrrd:
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 __del__(self):
if self.base_ref == None:
self.teem.nrrdNuke(self._ctypesobj)
else:
self.teem.nrrdNix(self._ctypesobj)
self.base_ref = None
self.teem = None
def __get_array_interface(self):
nrrd = self._ctypesobj.contents
s = []
for i in reversed(range(nrrd.dim)):
s.append(nrrd.axis[i].size)
r = {'shape': tuple(s),
'typestr': teemTypeToNumpyType(nrrd.type),
'data': (nrrd.data, False),
'version': 3}
return r
__array_interface__ = property(__get_array_interface)
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 save(self, file, args=None):
teem.nrrdSave(file, self._ctypesobj, args)
class ExtendedArray(numpy.ndarray):
def __new__(cls, input_array, base_ref=None):
if isinstance(input_array, Nrrd):
if input_array.base_ref == None:
obj = numpy.asarray(input_array).view(cls)
obj.base_ref = input_array
else:
obj = numpy.asarray(input_array.base_ref).view(cls)
obj.base_ref = None
else:
obj = numpy.asarray(input_array).view(cls)
obj.base_ref = base_ref
return obj
def __array_finalize__(self, obj):
if obj is None: return
self.base_ref = getattr(obj, 'base_ref', None)
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