def to_itk_image(image_like):
if isinstance(image_like, itk.Image):
return image_like
if is_arraylike(image_like):
array = np.asarray(image_like)
can_use_view = array.flags['OWNDATA']
if have_dask and isinstance(image_like, dask.array.core.Array):
can_use_view = False
array = np.ascontiguousarray(array)
# JavaScript does not support 64-bit integers
if array.dtype == np.int64:
array = array.astype(np.float32)
elif array.dtype == np.uint64:
array = array.astype(np.float32)
if can_use_view:
image_from_array = itk.image_view_from_array(array)
else:
image_from_array = itk.image_from_array(array)
return image_from_array
elif have_vtk and isinstance(image_like, vtk.vtkImageData):
from vtk.util import numpy_support as vtk_numpy_support
array = vtk_numpy_support.vtk_to_numpy(
image_like.GetPointData().GetScalars())
array.shape = tuple(image_like.GetDimensions())[::-1]
image_from_array = itk.image_view_from_array(array)
image_from_array.SetSpacing(image_like.GetSpacing())
image_from_array.SetOrigin(image_like.GetOrigin())
return image_from_array
elif have_simpleitk and isinstance(image_like, sitk.Image):
array = sitk.GetArrayViewFromImage(image_like)
image_from_array = itk.image_view_from_array(array)
image_from_array.SetSpacing(image_like.GetSpacing())
image_from_array.SetOrigin(image_like.GetOrigin())
direction = image_like.GetDirection()
npdirection = np.asarray(direction)
npdirection = np.reshape(npdirection, (-1, 3))
itkdirection = itk.matrix_from_array(npdirection)
image_from_array.SetDirection(itkdirection)
return image_from_array
elif have_imagej:
import imglyb
if isinstance(image_like,
imglyb.util.ReferenceGuardingRandomAccessibleInterval):
array = imglyb.to_numpy(image_like)
image_from_array = itk.image_view_from_array(array)
return image_from_array
elif isinstance(image_like, itk.ProcessObject):
return itk.output(image_like)
return None
def validate(self, obj, value):
if is_arraylike(value):
array = np.asarray(value)
self._source_object = array
if array.flags['OWNDATA']:
image_from_array = itk.GetImageViewFromArray(array)
else:
image_from_array = itk.GetImageFromArray(array)
return image_from_array
elif have_vtk and isinstance(value, vtk.vtkImageData):
from vtk.util import numpy_support as vtk_numpy_support
array = vtk_numpy_support.vtk_to_numpy(
value.GetPointData().GetScalars())
array.shape = tuple(value.GetDimensions())[::-1]
self._source_object = array
image_from_array = itk.GetImageViewFromArray(array)
image_from_array.SetSpacing(value.GetSpacing())
image_from_array.SetOrigin(value.GetOrigin())
return image_from_array
elif have_imglyb and isinstance(
value, imglyb.util.ReferenceGuardingRandomAccessibleInterval):
array = imglyb.to_numpy(value)
self._source_object = array
image_from_array = itk.GetImageViewFromArray(array)
return image_from_array
try:
# an itk.Image or a filter that produces an Image
# return itk.output(value)
# Working around traitlets / ipywidgets update mechanism to
# force an update. While the result of __eq__ can indicate it is
# the same object, the actual contents may have changed, as
# indicated by image.GetMTime()
value = itk.output(value)
self._source_object = value
grafted = value.__New_orig__()
grafted.Graft(value)
return grafted
except:
self.error(obj, value)
def view(image):
have_imglyb = False
try:
import imglyb
have_imglyb = True
except ImportError:
pass
have_vtk = False
try:
import vtk
have_vtk = True
except ImportError:
pass
viewer = Viewer()
if isinstance(image, np.ndarray):
image_from_array = itk.GetImageViewFromArray(image)
viewer.image = image_from_array
elif have_vtk and isinstance(image, vtk.vtkImageData):
from vtk.util import numpy_support as vtk_numpy_support
array = vtk_numpy_support.vtk_to_numpy(
image.GetPointData().GetScalars())
array.shape = tuple(image.GetDimensions())[::-1]
image_from_array = itk.GetImageViewFromArray(array)
image_from_array.SetSpacing(image.GetSpacing())
image_from_array.SetOrigin(image.GetOrigin())
viewer.image = image_from_array
elif have_imglyb and isinstance(
image, imglyb.util.ReferenceGuardingRandomAccessibleInterval):
image_array = imglyb.to_numpy(image)
print(image_array)
image_from_array = itk.GetImageViewFromArray(image_array)
else:
# an itk.Image
viewer.image = image
return viewer
def to_itk_image(image_like):
if isinstance(image_like, (itk.Image, itk.VectorImage)):
return image_like
if is_arraylike(image_like):
array = np.asarray(image_like)
can_use_view = array.flags['OWNDATA']
if have_dask and isinstance(image_like, dask.array.core.Array):
can_use_view = False
array = np.ascontiguousarray(array)
# JavaScript does not support 64-bit integers
if array.dtype == np.int64:
array = array.astype(np.float32)
elif array.dtype == np.uint64:
array = array.astype(np.float32)
if can_use_view:
image_from_array = itk.image_view_from_array(array)
else:
image_from_array = itk.image_from_array(array)
return image_from_array
elif have_vtk and isinstance(image_like, vtk.vtkImageData):
from vtk.util import numpy_support as vtk_numpy_support
array = vtk_numpy_support.vtk_to_numpy(
image_like.GetPointData().GetScalars())
dims = list(image_like.GetDimensions())
spacing = list(image_like.GetSpacing())
origin = list(image_like.GetOrigin())
# Check for zdim==1
zdim = dims.pop()
if zdim > 1:
# zdim>1, put it back in the dims array
dims.append(zdim)
else:
#zdim==1, remove z-spacing and z-origin
spacing.pop()
origin.pop()
array.shape = dims[::-1]
image_from_array = itk.image_view_from_array(array)
image_from_array.SetSpacing(spacing)
image_from_array.SetOrigin(origin)
return image_from_array
elif have_simpleitk and isinstance(image_like, sitk.Image):
array = sitk.GetArrayViewFromImage(image_like)
image_from_array = itk.image_view_from_array(array)
image_from_array.SetSpacing(image_like.GetSpacing())
image_from_array.SetOrigin(image_like.GetOrigin())
direction = image_like.GetDirection()
npdirection = np.asarray(direction)
npdirection = np.reshape(npdirection, (-1, image_like.GetDimension()))
itkdirection = itk.matrix_from_array(npdirection)
image_from_array.SetDirection(itkdirection)
return image_from_array
elif have_imagej:
import imglyb
if isinstance(image_like,
imglyb.util.ReferenceGuardingRandomAccessibleInterval):
array = imglyb.to_numpy(image_like)
image_from_array = itk.image_view_from_array(array)
return image_from_array
elif isinstance(image_like, itk.ProcessObject):
return itk.output(image_like)
return None