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/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#if SWIGPYTHON
%begin %{
#include "sitkPython.h"
%}
%{
#include "sitkPyCommand.h"
%}
%include "PythonDocstrings.i"
// ignore overload methods of int type when there is an enum
%ignore itk::simple::CastImageFilter::SetOutputPixelType( PixelIDValueType pixelID );
%ignore itk::simple::GetPixelIDValueAsString( PixelIDValueType type );
// Make __str__ transparent by renaming ToString to __str__
%rename(__str__) ToString;
%rename( __GetPixelAsInt8__ ) itk::simple::Image::GetPixelAsInt8;
%rename( __GetPixelAsUInt8__ ) itk::simple::Image::GetPixelAsUInt8;
%rename( __GetPixelAsInt16__ ) itk::simple::Image::GetPixelAsInt16;
%rename( __GetPixelAsUInt16__ ) itk::simple::Image::GetPixelAsUInt16;
%rename( __GetPixelAsInt32__ ) itk::simple::Image::GetPixelAsInt32;
%rename( __GetPixelAsUInt32__ ) itk::simple::Image::GetPixelAsUInt32;
%rename( __GetPixelAsInt64__ ) itk::simple::Image::GetPixelAsInt64;
%rename( __GetPixelAsUInt64__ ) itk::simple::Image::GetPixelAsUInt64;
%rename( __GetPixelAsFloat__ ) itk::simple::Image::GetPixelAsFloat;
%rename( __GetPixelAsDouble__ ) itk::simple::Image::GetPixelAsDouble;
%rename( __GetPixelAsVectorInt8__ ) itk::simple::Image::GetPixelAsVectorInt8;
%rename( __GetPixelAsVectorUInt8__ ) itk::simple::Image::GetPixelAsVectorUInt8;
%rename( __GetPixelAsVectorInt16__ ) itk::simple::Image::GetPixelAsVectorInt16;
%rename( __GetPixelAsVectorUInt16__ ) itk::simple::Image::GetPixelAsVectorUInt16;
%rename( __GetPixelAsVectorInt32__ ) itk::simple::Image::GetPixelAsVectorInt32;
%rename( __GetPixelAsVectorUInt32__ ) itk::simple::Image::GetPixelAsVectorUInt32;
%rename( __GetPixelAsVectorInt64__ ) itk::simple::Image::GetPixelAsVectorInt64;
%rename( __GetPixelAsVectorUInt64__ ) itk::simple::Image::GetPixelAsVectorUInt64;
%rename( __GetPixelAsVectorFloat32__ ) itk::simple::Image::GetPixelAsVectorFloat32;
%rename( __GetPixelAsVectorFloat64__ ) itk::simple::Image::GetPixelAsVectorFloat64;
%rename( __GetPixelAsComplexFloat32__ ) itk::simple::Image::GetPixelAsComplexFloat32;
%rename( __GetPixelAsComplexFloat64__ ) itk::simple::Image::GetPixelAsComplextFloat64;
%rename( __SetPixelAsInt8__ ) itk::simple::Image::SetPixelAsInt8;
%rename( __SetPixelAsUInt8__ ) itk::simple::Image::SetPixelAsUInt8;
%rename( __SetPixelAsInt16__ ) itk::simple::Image::SetPixelAsInt16;
%rename( __SetPixelAsUInt16__ ) itk::simple::Image::SetPixelAsUInt16;
%rename( __SetPixelAsInt32__ ) itk::simple::Image::SetPixelAsInt32;
%rename( __SetPixelAsUInt32__ ) itk::simple::Image::SetPixelAsUInt32;
%rename( __SetPixelAsInt64__ ) itk::simple::Image::SetPixelAsInt64;
%rename( __SetPixelAsUInt64__ ) itk::simple::Image::SetPixelAsUInt64;
%rename( __SetPixelAsFloat__ ) itk::simple::Image::SetPixelAsFloat;
%rename( __SetPixelAsDouble__ ) itk::simple::Image::SetPixelAsDouble;
%rename( __SetPixelAsVectorInt8__ ) itk::simple::Image::SetPixelAsVectorInt8;
%rename( __SetPixelAsVectorUInt8__ ) itk::simple::Image::SetPixelAsVectorUInt8;
%rename( __SetPixelAsVectorInt16__ ) itk::simple::Image::SetPixelAsVectorInt16;
%rename( __SetPixelAsVectorUInt16__ ) itk::simple::Image::SetPixelAsVectorUInt16;
%rename( __SetPixelAsVectorInt32__ ) itk::simple::Image::SetPixelAsVectorInt32;
%rename( __SetPixelAsVectorUInt32__ ) itk::simple::Image::SetPixelAsVectorUInt32;
%rename( __SetPixelAsVectorInt64__ ) itk::simple::Image::SetPixelAsVectorInt64;
%rename( __SetPixelAsVectorUInt64__ ) itk::simple::Image::SetPixelAsVectorUInt64;
%rename( __SetPixelAsVectorFloat32__ ) itk::simple::Image::SetPixelAsVectorFloat32;
%rename( __SetPixelAsVectorFloat64__ ) itk::simple::Image::SetPixelAsVectorFloat64;
%rename( __SetPixelAsComplexFloat32__ ) itk::simple::Image::SetPixelAsComplexFloat32;
%rename( __SetPixelAsComplexFloat64__ ) itk::simple::Image::SetPixelAsComplextFloat64;
%pythoncode %{
import operator
import sys
%}
%extend itk::simple::Image {
%pythoncode %{
# mathematical operators
def __add__( self, other ):
if isinstance( other, Image ):
return Add( self, other )
try:
return Add( self, float(other) )
except ValueError:
return NotImplemented
def __sub__( self, other ):
if isinstance( other, Image ):
return Subtract( self, other )
try:
return Subtract( self, float(other) )
except ValueError:
return NotImplemented
def __mul__( self, other ):
if isinstance( other, Image ):
return Multiply( self, other )
try:
return Multiply( self, float(other) )
except ValueError:
return NotImplemented
def __div__( self, other ):
if isinstance( other, Image ):
return Divide( self, other )
try:
return Divide( self, float(other) )
except ValueError:
return NotImplemented
def __floordiv__( self, other ):
if isinstance( other, Image ):
return DivideFloor( self, other )
try:
return DivideFloor( self, float(other) )
except ValueError:
return NotImplemented
def __truediv__( self, other ):
if isinstance( other, Image ):
return DivideReal( self, other )
try:
return DivideReal( self, float(other) )
except ValueError:
return NotImplemented
def __neg__( self ):
return UnaryMinus( self )
def __pos__( self ):
return self
# NOTE: for the reverse methods other cannot be an image, so
# therefore other should be able to be considered a constant.
def __radd__( self, other ):
try:
return Add( float(other), self )
except ValueError:
return NotImplemented
def __rsub__( self, other ):
try:
return Subtract( float(other), self )
except ValueError:
return NotImplemented
def __rmul__( self, other ):
try:
return Multiply( float(other), self )
except ValueError:
return NotImplemented
def __rdiv__( self, other ):
try:
return Divide( float(other), self )
except ValueError:
return NotImplemented
def __rfloordiv__( self, other ):
try:
return DivideFloor( float(other), self )
except ValueError:
return NotImplemented
def __rtruediv__( self, other ):
try:
return DivideReal( float(other), self )
except ValueError:
return NotImplemented
# NOTE: the __i*__ methods are not implemented because there
# currently in no way to make the underlying filters run
# inplace. But python will implement a default version based
# on the standard method
def __iadd__ ( self, other ):
self = Add( self, other )
return self;
# logic operators
def __and__( self, other ):
if isinstance( other, Image ):
return And( self, other )
try:
return And( self, int(other) )
except ValueError:
return NotImplemented
def __rand__( self, other ):
try:
return And( int(other), self )
except ValueError:
return NotImplemented
def __or__( self, other ):
if isinstance( other, Image ):
return Or( self, other )
try:
return Or( self, int(other) )
except ValueError:
return NotImplemented
def __ror__( self, other ):
try:
return Or( int(other), self )
except ValueError:
return NotImplemented
def __xor__( self, other ):
if isinstance( other, Image ):
return Xor( self, other )
try:
return Xor( self, int(other) )
except ValueError:
return NotImplemented
def __rxor__( self, other ):
try:
return Xor( int(other), self )
except ValueError:
return NotImplemented
def __invert__( self ): return BitwiseNot( self )
# Relational and Equality operators
def __lt__( self, other ):
if isinstance( other, Image ):
return Less( self, other )
try:
return Less( self, float(other) )
except (ValueError, TypeError):
return NotImplemented
def __le__( self, other ):
if isinstance( other, Image ):
return LessEqual( self, other )
try:
return LessEqual( self, float(other) )
except (ValueError, TypeError):
return NotImplemented
def __eq__( self, other ):
if isinstance( other, Image ):
return Equal( self, other )
try:
return Equal( self, float(other) )
except (ValueError, TypeError):
return NotImplemented
def __ne__( self, other ):
if isinstance( other, Image ):
return NotEqual( self, other )
try:
return NotEqual( self, float(other) )
except (ValueError, TypeError):
return NotImplemented
def __gt__( self, other ):
if isinstance( other, Image ):
return Greater( self, other )
try:
return Greater( self, float(other) )
except (ValueError, TypeError):
return NotImplemented
def __ge__( self, other ):
if isinstance( other, Image ):
return GreaterEqual( self, other )
try:
return GreaterEqual( self, float(other) )
except (ValueError, TypeError):
return NotImplemented
# "function" operators
def __pow__( self, other ):
if isinstance( other, Image ):
return Pow( self, other )
try:
return Pow( self, float(other) )
except ValueError:
return NotImplemented
def __rpow__( self, other ):
try:
return Pow( float(other), self )
except ValueError:
return NotImplemented
def __mod__( self, other ): return Modulus( self, other )
def __abs__( self ): return Abs( self )
# iterator and container methods
def __iter__( self ):
if len(self) == 0:
raise StopIteration
dim = self.GetDimension()
size = self.GetSize()
idx = [0] * dim
while idx[dim-1] < size[dim-1]:
yield self[ idx ]
# increment the idx
for d in range( 0, dim ):
idx[d] += 1
if idx[d] >= size[d] and d != dim - 1:
idx[d] = 0
else:
break
return
def __len__( self ):
l = 1
for ds in self.GetSize():
l *= ds
return l
# set/get pixel methods
def __getitem__( self, idx ):
""" Get an pixel value or a sliced image.
This operator implements basic indexing where idx is
arguments or a squence of integers the same dimension as
the image. The result will be a pixel value from that
index.
Multi-dimension extended slice based indexing is also
implemented. The return is a copy of a new image. The
standard sliced based indices are supported including
negative indices, to indicate location relative to the
end, along with negative step sized to indicate reversing
of direction.
If the length of idx is less than the number of dimension
of the image it will be padded with the defaults slice
":".
A 2D image can be extracted from a 3D image by providing
one argument being an integer instead of a slice."""
if sys.version_info[0] < 3:
def isint( i ):
return type(i) == int or type(i) == long
else:
def isint( i ):
return type(i) == int
dim = self.GetDimension()
size = self.GetSize()
try:
if (len(idx) < dim):
# if the argument tuple has fewer elements then the dimension of the image then extend to match that of the image
idx = tuple(idx) + (slice(None),)*(dim-len(idx))
except TypeError:
# if the len function didn't work then, assume is a
# non-iterable, and make it a single element in a tuple.
idx = (idx,) + (slice(None),)*(dim-1)
if (len(idx) > dim):
raise IndexError("invalid index")
# All the indices are integers just return GetPixel value
if all( isint(i) for i in idx ):
# if any of the arguments are negative integers subract them for the size
idx = [idx[i] if idx[i] >= 0 else (size[i] + idx[i]) for i in range(len(idx))]
if any( idx[i] < 0 or idx[i] >= size[i] for i in range(len(idx))):
raise IndexError("index out of bounds")
return self.GetPixel(*tuple(idx))
# If we have a 3D image, we can extract 2D image if one index is an int and the reset are slices
slice_dim = -1
if ( dim == 3 ):
# find only a single dimension with has an integer index
for i in range(len(idx)):
if type(idx[i]) is slice:
continue
elif isint(idx[i]):
if(slice_dim == -1):
slice_dim = abs(i)
else:
slice_dim = -1
break
if slice_dim != -1:
# replace int slice_dim with a slice
s = idx[slice_dim]
if s < 0:
s += size[slice_dim]
if s < 0 or s >= size[slice_dim]:
raise IndexError("index out of bounds")
idx = tuple(idx[:slice_dim]) + (slice(s, s+1),)+ tuple(idx[slice_dim+1:])
# Use the slice filter when all the elements are slices ( or have been processed to be )
if all( type(i) is slice for i in idx ):
# perform standard slice indexing, to clamp to ranges and add in defaults
sidx = [ idx[i].indices(size[i]) for i in range(len(idx ))]
# extract each element of the indices rages together
(start, stop, step) = zip(*sidx)
# run the slice filter
img = Slice(self, start=start, stop=stop, step=step)
if (slice_dim != -1):
# the stop is on the wrong side of step
if any( (s[1]-s[0])//s[2] <= 0 for s in sidx ):
raise IndexError("invalid range")
size = img.GetSize();
# set the slice dimension size to 0
size = size[:slice_dim]+(0,)+size[slice_dim+1:]
# reduce the 3D image to a 2D
img = Extract( img, size )
return img
# the index parameter was an invalid set of objects
raise IndexError("invalid index")
def __setitem__( self, idx, value ):
"""Sets the pixel value at index idx to value.
The dimension of idx should match that of the image."""
if sys.version_info[0] < 3:
def isint( i ):
return type(i) == int or type(i) == long
else:
def isint( i ):
return type(i) == int
dim = self.GetDimension()
size = self.GetSize()
if (len(idx) > dim):
raise IndexError("invalid index")
# All the indices are integers just return SetPixel value
if all( isint(i) for i in idx ):
# if any of the arguments are negative integers subract them for the size
idx = [idx[i] if idx[i] >= 0 else (size[i] + idx[i]) for i in range(len(idx))]
if any( idx[i] < 0 or idx[i] >= size[i] for i in range(len(idx))):
raise IndexError("index out of bounds")
return self.SetPixel(*(tuple(idx)+(value,)))
# the index parameter was an invalid set of objects
raise IndexError("invalid index")
def GetPixel(self, *idx):
"""Returns the value of a pixel.
This method takes 2 parameters in 2D: the x and y index,
and 3 parameters in 3D: the x, y and z index."""
if len(idx) == 1:
idx = idx[0]
pixelID = self.GetPixelIDValue()
if pixelID == sitkUnknown:
raise Exception("invalid pixel type")
if pixelID == sitkInt8:
return self.__GetPixelAsInt8__( idx )
if pixelID == sitkUInt8 or pixelID == sitkLabelUInt8:
return self.__GetPixelAsUInt8__( idx )
if pixelID == sitkInt16:
return self.__GetPixelAsInt16__( idx )
if pixelID == sitkUInt16 or pixelID == sitkLabelUInt16:
return self.__GetPixelAsUInt16__( idx )
if pixelID == sitkInt32:
return self.__GetPixelAsInt32__( idx )
if pixelID == sitkUInt32 or pixelID == sitkLabelUInt32:
return self.__GetPixelAsUInt32__( idx )
if pixelID == sitkInt64:
return self.__GetPixelAsInt64__( idx )
if pixelID == sitkUInt64 or pixelID == sitkLabelUInt64:
return self.__GetPixelAsUInt64__( idx )
if pixelID == sitkFloat32:
return self.__GetPixelAsFloat__( idx )
if pixelID == sitkFloat64:
return self.__GetPixelAsDouble__( idx )
if pixelID == sitkVectorInt8:
return self.__GetPixelAsVectorInt8__( idx )
if pixelID == sitkVectorUInt8:
return self.__GetPixelAsVectorUInt8__( idx )
if pixelID == sitkVectorInt16:
return self.__GetPixelAsVectorInt16__( idx )
if pixelID == sitkVectorUInt16:
return self.__GetPixelAsVectorUInt16__( idx )
if pixelID == sitkVectorInt32:
return self.__GetPixelAsVectorInt32__( idx )
if pixelID == sitkVectorUInt32:
return self.__GetPixelAsVectorUInt32__( idx )
if pixelID == sitkVectorInt64:
return self.__GetPixelAsVectorInt64__( idx )
if pixelID == sitkVectorUInt64:
return self.__GetPixelAsVectorUInt64__( idx )
if pixelID == sitkVectorFloat32:
return self.__GetPixelAsVectorFloat32__( idx )
if pixelID == sitkVectorFloat64:
return self.__GetPixelAsVectorFloat64__( idx )
if pixelID == sitkComplexFloat32:
return self.__GetPixelAsComplexFloat32__( idx )
if pixelID == sitkComplexFloat64:
return self.__GetPixelAsComplexFloat64__( idx )
raise Exception("unknown pixel type")
def SetPixel(self, *args):
"""Sets the value of a pixel.
This method takes 3 parameters in 2D: the x and y index then the value,
and 4 parameters in 3D: the x, y and z index then the value."""
pixelID = self.GetPixelIDValue()
if pixelID == sitkUnknown:
raise Exception("invalid pixel type")
if len(args) < 2:
raise Exception( "Wrong number of arguments, coordinates arguments then value" )
idx = args[:len(args)-1]
if len(idx) == 1:
idx = idx[0]
value = args[-1]
if pixelID == sitkInt8:
return self.__SetPixelAsInt8__( idx, value )
if pixelID == sitkUInt8 or pixelID == sitkLabelUInt8:
return self.__SetPixelAsUInt8__( idx, value )
if pixelID == sitkInt16:
return self.__SetPixelAsInt16__( idx, value )
if pixelID == sitkUInt16 or pixelID == sitkLabelUInt16:
return self.__SetPixelAsUInt16__( idx, value )
if pixelID == sitkInt32:
return self.__SetPixelAsInt32__( idx, value )
if pixelID == sitkUInt32 or pixelID == sitkLabelUInt32:
return self.__SetPixelAsUInt32__( idx, value )
if pixelID == sitkInt64:
return self.__SetPixelAsInt64__( idx, value )
if pixelID == sitkUInt64 or pixelID == sitkLabelUInt64:
return self.__SetPixelAsUInt64__( idx, value )
if pixelID == sitkFloat32:
return self.__SetPixelAsFloat__( idx, value )
if pixelID == sitkFloat64:
return self.__SetPixelAsDouble__( idx, value )
if pixelID == sitkVectorInt8:
return self.__SetPixelAsVectorInt8__( idx, value )
if pixelID == sitkVectorUInt8:
return self.__SetPixelAsVectorUInt8__( idx, value )
if pixelID == sitkVectorInt16:
return self.__SetPixelAsVectorInt16__( idx, value )
if pixelID == sitkVectorUInt16:
return self.__SetPixelAsVectorUInt16__( idx, value )
if pixelID == sitkVectorInt32:
return self.__SetPixelAsVectorInt32__( idx, value )
if pixelID == sitkVectorUInt32:
return self.__SetPixelAsVectorUInt32__( idx, value )
if pixelID == sitkVectorInt64:
return self.__SetPixelAsVectorInt64__( idx, value )
if pixelID == sitkVectorUInt64:
return self.__SetPixelAsVectorUInt64__( idx, value )
if pixelID == sitkVectorFloat32:
return self.__SetPixelAsVectorFloat32__( idx, value )
if pixelID == sitkVectorFloat64:
return self.__SetPixelAsVectorFloat64__( idx, value )
if pixelID == sitkComplexFloat32:
return self.__SetPixelAsComplexFloat32__( idx, value )
if pixelID == sitkComplexFloat64:
return self.__SetPixelAsComplexFloat64__( idx, value )
raise Exception("unknown pixel type")
%}
}
// This is included inline because SwigMethods (SimpleITKPYTHON_wrap.cxx)
// is declared static.
%{
#include "sitkNumpyArrayConversion.cxx"
%}
// Numpy array conversion support
%native(_GetMemoryViewFromImage) PyObject *sitk_GetMemoryViewFromImage( PyObject *self, PyObject *args );
%native(_SetImageFromArray) PyObject *sitk_SetImageFromArray( PyObject *self, PyObject *args );
%pythoncode %{
HAVE_NUMPY = True
try:
import numpy
except ImportError:
HAVE_NUMPY = False
def _get_numpy_dtype( sitkImage ):
"""Given a SimpleITK image, returns the numpy.dtype which describes the data"""
if not HAVE_NUMPY:
raise ImportError('Numpy not available.')
# this is a mapping from sitk's pixel id to numpy's dtype
_sitk_np = {sitkUInt8:numpy.uint8,
sitkUInt16:numpy.uint16,
sitkUInt32:numpy.uint32,
sitkUInt64:numpy.uint64,
sitkInt8:numpy.int8,
sitkInt16:numpy.int16,
sitkInt32:numpy.int32,
sitkInt64:numpy.int64,
sitkFloat32:numpy.float32,
sitkFloat64:numpy.float64,
sitkComplexFloat32:numpy.complex64,
sitkComplexFloat64:numpy.complex128,
sitkVectorUInt8:numpy.uint8,
sitkVectorInt8:numpy.int8,
sitkVectorUInt16:numpy.uint16,
sitkVectorInt16:numpy.int16,
sitkVectorUInt32:numpy.uint32,
sitkVectorInt32:numpy.int32,
sitkVectorUInt64:numpy.uint64,
sitkVectorInt64:numpy.int64,
sitkVectorFloat32:numpy.float32,
sitkVectorFloat64:numpy.float64,
sitkLabelUInt8:numpy.uint8,
sitkLabelUInt16:numpy.uint16,
sitkLabelUInt32:numpy.uint32,
sitkLabelUInt64:numpy.uint64
}
return _sitk_np[ sitkImage.GetPixelIDValue() ]
def _get_sitk_pixelid(numpy_array_type):
"""Returns a SimpleITK PixelID given a numpy array."""
if not HAVE_NUMPY:
raise ImportError('Numpy not available.')
# This is a Mapping from numpy array types to sitks pixel types.
_np_sitk = {numpy.character:sitkUInt8,
numpy.uint8:sitkUInt8,
numpy.uint16:sitkUInt16,
numpy.uint32:sitkUInt32,
numpy.uint64:sitkUInt64,
numpy.int8:sitkInt8,
numpy.int16:sitkInt16,
numpy.int32:sitkInt32,
numpy.int64:sitkInt64,
numpy.float32:sitkFloat32,
numpy.float64:sitkFloat64,
numpy.complex64:sitkComplexFloat32,
numpy.complex128:sitkComplexFloat64
}
try:
return _np_sitk[numpy_array_type.dtype]
except KeyError:
for key in _np_sitk:
if numpy.issubdtype(numpy_array_type.dtype, key):
return _np_sitk[key]
def _get_sitk_vector_pixelid(numpy_array_type):
"""Returns a SimpleITK vecotr PixelID given a numpy array."""
if not HAVE_NUMPY:
raise ImportError('Numpy not available.')
# This is a Mapping from numpy array types to sitks pixel types.
_np_sitk = {numpy.character:sitkVectorUInt8,
numpy.uint8:sitkVectorUInt8,
numpy.uint16:sitkVectorUInt16,
numpy.uint32:sitkVectorUInt32,
numpy.uint64:sitkVectorUInt64,
numpy.int8:sitkVectorInt8,
numpy.int16:sitkVectorInt16,
numpy.int32:sitkVectorInt32,
numpy.int64:sitkVectorInt64,
numpy.float32:sitkVectorFloat32,
numpy.float64:sitkVectorFloat64,
}
try:
return _np_sitk[numpy_array_type.dtype]
except KeyError:
for key in _np_sitk:
if numpy.issubdtype(numpy_array_type.dtype, key):
return _np_sitk[key]
# SimplyITK <-> Numpy Array conversion support.
def GetArrayViewFromImage(image):
"""Get a NumPy ndarray view of a SimpleITK Image.
Returns a Numpy ndarray object as a "view" of the SimpleITK's Image buffer. This reduces pixel buffer copies, but requires that the SimpleITK image object is kept around while the buffer is being used.
"""
if not HAVE_NUMPY:
raise ImportError('NumPy not available.')
pixelID = image.GetPixelIDValue()
assert pixelID != sitkUnknown, "An SimpleITK image of Unknown pixel type should not exists!"
dtype = _get_numpy_dtype( image )
shape = image.GetSize();
if image.GetNumberOfComponentsPerPixel() > 1:
shape = ( image.GetNumberOfComponentsPerPixel(), ) + shape
image.MakeUnique()
imageMemoryView = _SimpleITK._GetMemoryViewFromImage(image)
arrayView = numpy.asarray(imageMemoryView).view(dtype = dtype)
arrayView.shape = shape[::-1]
return arrayView
def GetArrayFromImage(image):
"""Get a NumPy ndarray from a SimpleITK Image.
This is a deep copy of the image buffer and is completely safe and without potential side effects.
"""
# TODO: If the image is already not unique then a second copy may be made before the numpy copy is done.
arrayView = GetArrayViewFromImage(image)
# perform deep copy of the image buffer
return numpy.array(arrayView, copy=True)
def GetImageFromArray( arr, isVector=False):
"""Get a SimpleITK Image from a numpy array. If isVector is True, then a 3D array will be treated as a 2D vector image, otherwise it will be treated as a 3D image"""
if not HAVE_NUMPY:
raise ImportError('Numpy not available.')
z = numpy.asarray( arr )
assert z.ndim in ( 2, 3, 4 ), \
"Only arrays of 2, 3 or 4 dimensions are supported."
if ( z.ndim == 3 and isVector ) or (z.ndim == 4):
id = _get_sitk_vector_pixelid( z )
img = Image( z.shape[-2::-1] , id, z.shape[-1] )
elif z.ndim in ( 2, 3 ):
id = _get_sitk_pixelid( z )
img = Image( z.shape[::-1], id )
_SimpleITK._SetImageFromArray( z.tostring(), img )
return img
%}
// Enable Java classes derived from Command Execute method to be
// called from C++
%feature("director") itk::simple::Command;
%extend itk::simple::ProcessObject {
int AddCommand( itk::simple::EventEnum e, PyObject *obj )
{
if (!PyCallable_Check(obj))
{
return 0;
}
itk::simple::PyCommand *cmd = NULL;
try
{
cmd = new itk::simple::PyCommand();
cmd->SetCallbackPyCallable(obj);
int ret = self->AddCommand(e,*cmd);
cmd->OwnedByProcessObjectsOn();
return ret;
}
catch(...)
{
delete cmd;
throw;
}
}
};
#endif
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